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analysis.bundled.js
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analysis.bundled.js
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d.PageLayoutView(t.extend(i,{el:"body",left:p,center:g,right:f}));Galaxy.page=m,Galaxy.params=Galaxy.config.params,Galaxy.toolPanel=p.tool_panel,Galaxy.upload=p.uploadButton,Galaxy.currHistoryPanel=f.historyView,Galaxy.currHistoryPanel.listenToGalaxy(Galaxy),Galaxy.app={display:function(t,e){s(".select2-hidden-accessible").remove(),g.display(t)}};new(e.Router.extend({initialize:function(t){this.options=t},execute:function(t,e,i){Galaxy.debug("router execute:",t,e,i);var n=a.parse(e.pop());e.push(n),t&&t.apply(this,e)},routes:{"(/)":"home","(/)root*":"home"},home:function(t){(t.tool_id||t.job_id)&&"upload1"!==t.tool_id?this._loadToolForm(t):t.workflow_id?this._loadCenterIframe("workflow/run?id="+t.workflow_id):t.m_c?this._loadCenterIframe(t.m_c+"/"+t.m_a):this._loadCenterIframe("welcome")},_loadToolForm:function(t){t.id=t.tool_id,g.display(new 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missing.");this.url_viz=s.get("url_viz"),s.get("genome_build")&&(this.genome_build=s.get("genome_build"));var a=new i.IconButtonView({model:new i.IconButton({title:"Visualize",icon_class:"chart_curve",id:"btn_viz"})});this.setElement(t.$el),this.$el.append(a.render().$el),this.hide()}}}},events:{"mouseover tr":"show",mouseleave:"hide"},show:function(t){function e(t){return!isNaN(parseFloat(t))&&isFinite(t)}if(null!==this.col.chrom){var i=r(t.target).parent(),n=i.children().eq(this.col.chrom).html(),s=i.children().eq(this.col.start).html(),o=this.col.end?i.children().eq(this.col.end).html():s;if(!n.match("^#")&&""!==n&&e(s)){var a={dataset_id:this.dataset_id,gene_region:n+":"+s+"-"+o},l=i.offset(),c=l.left-10,d=l.top-r(window).scrollTop()+3;r("#btn_viz").css({position:"fixed",top:d+"px",left:c+"px"}),r("#btn_viz").off("click"),r("#btn_viz").click(this.create_trackster_action(this.url_viz,a,this.genome_build)),r("#btn_viz").show()}else r("#btn_viz").hide()}},hide:function(){this.$el.find("#btn_viz").hide()},create_trackster_action:function(t,e,i){var n=this;return function(){var s={};return i&&(s["f-dbkey"]=i),r.ajax({url:t+"/list_tracks?"+r.param(s),dataType:"html",error:function(){n.modal.show({title:"Something went wrong!",body:"Unfortunately we could not add this dataset to the track browser. Please try again or contact us.",buttons:{Cancel:function(){n.modal.hide()}}})},success:function(i){n.modal.show({title:"View Data in a New or Saved Visualization",buttons:{Cancel:function(){n.modal.hide()},"View in saved visualization":function(){n.modal.show({title:"Add Data to Saved Visualization",body:i,buttons:{Cancel:function(){n.modal.hide()},"Add to visualization":function(){n.modal.hide(),n.modal.$el.find("input[name=id]:checked").each(function(){var i=r(this).val();e.id=i,n.frame.add({title:"Trackster",type:"url",content:t+"/trackster?"+r.param(e)})})}}})},"View in new visualization":function(){n.modal.hide(),n.frame.add({title:"Trackster",type:"url",content:t+"/trackster?"+r.param(e)})}}})}}),!1}}}),g=function(t){t.model||(t.model=new l(t.dataset_config));var e=t.parent_elt,i=t.embedded;delete t.embedded,delete t.parent_elt,delete t.dataset_config;var n=i?new u(t):new h(t);return n.render(),e&&(e.append(n.$el),n.expand_to_container()),n};return{Dataset:s,TabularDataset:l,DatasetCollection:c,TabularDatasetChunkedView:d,createTabularDatasetChunkedView:g}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(3),i(1))},function(t,e,i){var n,s;n=[],s=function(){"use strict";var t={UPLOAD:"upload",QUEUED:"queued",RUNNING:"running",SETTING_METADATA:"setting_metadata",NEW:"new",EMPTY:"empty",OK:"ok",PAUSED:"paused",FAILED_METADATA:"failed_metadata",NOT_VIEWABLE:"noPermission",DISCARDED:"discarded",ERROR:"error"};return t.READY_STATES=[t.OK,t.EMPTY,t.PAUSED,t.FAILED_METADATA,t.NOT_VIEWABLE,t.DISCARDED,t.ERROR],t.NOT_READY_STATES=[t.UPLOAD,t.QUEUED,t.RUNNING,t.SETTING_METADATA,t.NEW],t}.apply(e,n),!(void 0!==s&&(t.exports=s))},function(t,e,i){var n,s;(function(o,a){n=[i(4)],s=function(t){var e=o.View.extend({initialize:function(e){this.options=t.merge(e,{id:t.uid(),title:"",floating:"right",icon:"",cls:"ui-button btn btn-default",cls_wait:"btn 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'),e+='<span class="title">'+t.title+"</span></button>"}}),i=e.extend({initialize:function(t){e.prototype.initialize.call(this,t)},_template:function(t){return'<a id="'+t.id+'" class="'+t.cls+'" href="'+(t.href||"javascript:void(0)")+'" title="'+t.title+'" target="'+(t.target||"_top")+'"><span class="'+t.icon+'"/></a>'}}),n=o.View.extend({initialize:function(e){this.options=t.merge(e,{title:"Select/Unselect all",icons:["fa fa-square-o","fa fa-minus-square-o","fa fa-check-square-o"],value:0}),this.setElement(this._template()),this.$title=this.$(".title"),this.$icon=this.$(".icon"),this.value(this.options.value),this.$title.html(this.options.title);var i=this;this.$el.on("click",function(){i.current=0===i.current&&2||0,i.value(i.current),i.options.onclick&&i.options.onclick()})},value:function(t,e){return void 0!==t&&(e&&0!==t&&(t=t!==e&&1||2),this.current=t,this.$icon.removeClass().addClass("icon").addClass(this.options.icons[t]),this.options.onchange&&this.options.onchange(t)),this.current},_template:function(){return'<div class="ui-button-check" ><span class="icon"/><span class="title"/></div>'}}),s=o.View.extend({initialize:function(e){this.options=t.merge(e,{id:t.uid(),title:"",floating:"right",cls:"ui-button-icon",icon:"",tooltip:"",onclick:null}),this.setElement(this._template(this.options)),this.$button=this.$el.find(".button");var i=this;a(this.el).on("click",function(){a(".tooltip").hide(),e.onclick&&!i.disabled&&e.onclick()}),this.$button.tooltip({title:e.tooltip,placement:"bottom"})},disable:function(){this.$button.addClass("disabled"),this.disabled=!0},enable:function(){this.$button.removeClass("disabled"),this.disabled=!1},setIcon:function(t){this.$("i").removeClass(this.options.icon).addClass(t),this.options.icon=t},_template:function(t){var e="";t.title&&(e="width: 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t.title&&(n+=' <span class="title">'+t.title+"</span>"),n+="</div></div>"}});return{ButtonDefault:e,ButtonLink:i,ButtonIcon:s,ButtonCheck:n,ButtonMenu:r}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(1))},function(t,e,i){var n,s;(function(o,a){n=[i(4)],s=function(t){var e=o.View.extend({row:null,row_count:0,optionsDefault:{content:"No content available.",onchange:null,ondblclick:null,onconfirm:null,cls:"ui-table",cls_tr:""},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(e){this.options=t.merge(e,this.optionsDefault);var i=a(this._template(this.options));this.$thead=i.find("thead"),this.$tbody=i.find("tbody"),this.$tmessage=i.find("tmessage"),this.setElement(i),this.row=this._row()},addHeader:function(t){var e=a("<th></th>");e.append(t),this.row.append(e)},appendHeader:function(){this.$thead.append(this.row),this.row=a("<tr></tr>")},add:function(t,e,i){var 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e=o.View.extend({optionsDefault:{with_close:!0,title:null,placement:"top",container:"body",body:null},initialize:function(e){this.setElement(this._template()),this.uid=t.uid(),this.options=a.defaults(e||{},this.optionsDefault),this.options.container.parent().append(this.el),this.$title=this.$(".popover-title-label"),this.$close=this.$(".popover-close"),this.$body=this.$(".popover-content"),this.options.body&&this.append(this.options.body);var i=this;r("body").on("mousedown."+this.uid,function(t){i.visible&&!r(i.options.container).is(t.target)&&!r(i.el).is(t.target)&&0===r(i.el).has(t.target).length&&i.hide()})},render:function(){this.$title.html(this.options.title),this.$el.removeClass().addClass("ui-popover popover fade in").addClass(this.options.placement),this.$el.css(this._get_placement(this.options.placement));var t=this;this.options.with_close?this.$close.on("click",function(){t.hide()}).show():this.$close.off().hide()},title:function(t){void 0!==t&&(this.options.title=t,this.$title.html(t))},show:function(){this.render(),this.$el.show(),this.visible=!0},hide:function(){this.$el.hide(),this.visible=!1},append:function(t){this.$body.append(t)},empty:function(){this.$body.empty()},remove:function(){r("body").off("mousedown."+this.uid),this.$el.remove()},_get_placement:function(t){var e=this._get_width(this.$el),i=this.$el.height(),n=this.options.container,s=this._get_width(n),o=this._get_height(n),a=n.position(),r=left=0;if(-1!=["top","bottom"].indexOf(t))switch(left=a.left-e+(s+e)/2,t){case"top":r=a.top-i-5;break;case"bottom":r=a.top+o+5}else switch(r=a.top-i+(o+i)/2,t){case"right":left=a.left+s}return{top:r,left:left}},_get_width:function(t){return t.width()+parseInt(t.css("padding-left"))+parseInt(t.css("margin-left"))+parseInt(t.css("padding-right"))+parseInt(t.css("margin-right"))},_get_height:function(t){return t.height()+parseInt(t.css("padding-top"))+parseInt(t.css("padding-bottom"))},_template:function(t){return'<div class="ui-popover popover fade in"><div class="arrow"/><div class="popover-title"><div class="popover-title-label"/><div class="popover-close fa fa-times-circle"/></div><div class="popover-content"/></div>'}});return{View:e}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(3),i(1))},function(t,e,i){var n,s;(function(o){n=[i(4)],s=function(t){var e=o.View.extend({optionsDefault:{css:"",placeholder:"No data available",data:[],value:null,multiple:!1,minimumInputLength:0,initialData:""},initialize:function(e){if(this.options=t.merge(e,this.optionsDefault),this.setElement(this._template(this.options)),!this.options.container)return void console.log("ui-select::initialize() : container not specified.");if(this.options.container.append(this.$el),this.select_data=this.options.data,this._refresh(),!this.options.multiple){this.options.value&&this._setValue(this.options.value);var i=this;this.options.onchange&&this.$el.on("change",function(){i.options.onchange(i.value())})}},value:function(t){var e=this._getValue();void 0!==t&&this._setValue(t);var i=this._getValue();return i!=e&&this.options.onchange&&this.options.onchange(i),i},text:function(){return this.$el.select2("data").text},disabled:function(){return!this.$el.select2("enable")},enable:function(){this.$el.select2("enable",!0)},disable:function(){this.$el.select2("enable",!1)},add:function(t){this.select_data.push({id:t.id,text:t.text}),this._refresh()},del:function(t){var e=this._getIndex(t);-1!=e&&(this.select_data.splice(e,1),this._refresh())},remove:function(){this.$el.select2("destroy")},update:function(t){this.select_data=[];for(var e in t.data)this.select_data.push(t.data[e]);this._refresh()},_refresh:function(){if(this.options.multiple){var t={multiple:this.options.multiple,containerCssClass:this.options.css,placeholder:this.options.placeholder,minimumInputLength:this.options.minimumInputLength,ajax:this.options.ajax,dropdownCssClass:this.options.dropdownCssClass,escapeMarkup:this.options.escapeMarkup,formatResult:this.options.formatResult,formatSelection:this.options.formatSelection,initSelection:this.options.initSelection,initialData:this.options.initialData};this.$el.select2(t)}else{var e=this._getValue(),t={data:this.select_data,containerCssClass:this.options.css,placeholder:this.options.placeholder,dropdownAutoWidth:!0};this.$el.select2(t),this._setValue(e)}},_getIndex:function(t){for(var e in this.select_data)if(this.select_data[e].id==t)return e;return-1},_getValue:function(){return this.$el.select2("val")},_setValue:function(t){var e=this._getIndex(t);-1==e&&this.select_data.length>0&&(t=this.select_data[0].id),this.$el.select2("val",t)},_template:function(t){return'<input type="hidden" value="'+this.options.initialData+'"/>'}});return{View:e}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2))},function(t,e,i){var n,s;(function(o,a,r){n=[i(4)],s=function(t){var e=o.View.extend({optionsDefault:{title_new:"",operations:null,onnew:null,max:null,onchange:null},initialize:function(e){this.visible=!1,this.$nav=null,this.$content=null,this.first_tab=null,this.current_id=null,this.options=t.merge(e,this.optionsDefault);var i=a(this._template(this.options));this.$nav=i.find(".tab-navigation"),this.$content=i.find(".tab-content"),this.setElement(i),this.list={};var n=this;if(this.options.operations&&a.each(this.options.operations,function(t,e){e.$el.prop("id",t),n.$nav.find(".operations").append(e.$el)}),this.options.onnew){var s=a(this._template_tab_new(this.options));this.$nav.append(s),s.tooltip({title:"Add a new tab",placement:"bottom",container:n.$el}),s.on("click",function(t){s.tooltip("hide"),n.options.onnew()})}},size:function(){return r.size(this.list)},current:function(){return this.$el.find(".tab-pane.active").attr("id")},add:function(t){var e=this,i=t.id,n=a(this._template_tab(t)),s=a(this._template_tab_content(t));if(this.list[i]=t.ondel?!0:!1,this.options.onnew?this.$nav.find("#new-tab").before(n):this.$nav.append(n),s.append(t.$el),this.$content.append(s),1==this.size()&&(n.addClass("active"),s.addClass("active"),this.first_tab=i),this.options.max&&this.size()>=this.options.max&&this.$el.find("#new-tab").hide(),t.ondel){var o=n.find("#delete");o.tooltip({title:"Delete this tab",placement:"bottom",container:e.$el}),o.on("click",function(){return o.tooltip("destroy"),e.$el.find(".tooltip").remove(),t.ondel(),!1})}n.on("click",function(n){n.preventDefault(),t.onclick?t.onclick():e.show(i)}),this.current_id||(this.current_id=i)},del:function(t){this.$el.find("#tab-"+t).remove(),this.$el.find("#"+t).remove(),this.first_tab==t&&(this.first_tab=null),null!=this.first_tab&&this.show(this.first_tab),this.list[t]&&delete this.list[t],this.size()<this.options.max&&this.$el.find("#new-tab").show()},delRemovable:function(){for(var t in this.list)this.del(t)},show:function(t){this.$el.fadeIn("fast"),this.visible=!0,t&&(this.$el.find("#tab-"+this.current_id).removeClass("active"),this.$el.find("#"+this.current_id).removeClass("active"),this.$el.find("#tab-"+t).addClass("active"),this.$el.find("#"+t).addClass("active"),this.current_id=t),this.options.onchange&&this.options.onchange(t)},hide:function(){this.$el.fadeOut("fast"),this.visible=!1},hideOperation:function(t){this.$nav.find("#"+t).hide()},showOperation:function(t){this.$nav.find("#"+t).show()},setOperation:function(t,e){var i=this.$nav.find("#"+t);i.off("click"),i.on("click",e)},title:function(t,e){var i=this.$el.find("#tab-title-text-"+t);return e&&i.html(e),i.html()},retitle:function(t){var e=0;for(var i in this.list)this.title(i,++e+": "+t)},_template:function(t){return'<div class="ui-tabs tabbable tabs-left"><ul id="tab-navigation" class="tab-navigation nav nav-tabs"><div class="operations" style="float: right; margin-bottom: 4px;"></div></ul><div id="tab-content" class="tab-content"/></div>'},_template_tab_new:function(t){return'<li id="new-tab"><a href="javascript:void(0);"><i class="ui-tabs-add fa fa-plus-circle"/>'+t.title_new+"</a></li>"},_template_tab:function(t){var e='<li id="tab-'+t.id+'" class="tab-element"><a id="tab-title-link-'+t.id+'" title="" href="#'+t.id+'" data-original-title=""><span id="tab-title-text-'+t.id+'" class="tab-title-text">'+t.title+"</span>";return t.ondel&&(e+='<i id="delete" class="ui-tabs-delete fa fa-minus-circle"/>'),e+="</a></li>"},_template_tab_content:function(t){return'<div id="'+t.id+'" class="tab-pane"/>'}});return{View:e}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(1),i(3))},function(t,e){function i(t){function e(t){s.push(t)}if("string"==typeof t){var n={},s=[],o=i.call(n,e);return o.parse(t),{entries:s,errors:o.getErrors()}}if("function"!=typeof t)throw"Invalid parser construction.";return this.STATES_={ENTRY_OR_JUNK:0,OBJECT_TYPE:1,ENTRY_KEY:2,KV_KEY:3,EQUALS:4,KV_VALUE:5},this.DATA_={},this.CALLBACK_=t,this.CHAR_=0,this.LINE_=1,this.CHAR_IN_LINE_=0,this.SKIPWS_=!0,this.SKIPCOMMENT_=!0,this.PARSETMP_={},this.SKIPTILLEOL_=!1,this.VALBRACES_=null,this.BRACETYPE_=null,this.BRACECOUNT_=0,this.STATE_=this.STATES_.ENTRY_OR_JUNK,this.ERRORS_=[],this.ENTRY_TYPES_={inproceedings:1,proceedings:2,article:3,techreport:4,misc:5,mastersthesis:6,book:7,phdthesis:8,incollection:9,unpublished:10,inbook:11,manual:12,periodical:13,booklet:14,masterthesis:15,conference:16,online:998,data:999},this.MACROS_={jan:"January",feb:"February",mar:"March",apr:"April",may:"May",jun:"June",jul:"July",aug:"August",sep:"September",oct:"October",nov:"November",dec:"December",Jan:"January",Feb:"February",Mar:"March",Apr:"April",May:"May",Jun:"June",Jul:"July",Aug:"August",Sep:"September",Oct:"October",Nov:"November",Dec:"December"},this.getErrors=function(){return this.ERRORS_},this.parse=function(t){for(var e=0;e<t.length;e++)this.processCharacter_(t[e])},this.error_=function(t){this.ERRORS_.push([this.LINE_,this.CHAR_IN_LINE_,this.CHAR_,t])},this.processEntry_=function(){var t=this.DATA_;if(t.Fields)for(var e in t.Fields){for(var i=t.Fields[e],n=0;n<this.CHARCONV_.length;n++){var s=this.CHARCONV_[n][0],o=this.CHARCONV_[n][1];i=i.replace(s,o)}i=i.replace(/[\n\r\t]/g," ").replace(/\s\s+/g," ").replace(/^\s+|\s+$/g,"");for(var a=i.length,r="",n=0;a>n;n++){var l=i[n],c=!1;"\\"==l&&a-1>n?l=i[++n]:("{"==l||"}"==l)&&(c=!0),c||(r+=l)}t.Fields[e]=r}if("string"==t.ObjectType)for(var e in t.Fields)this.MACROS_[e]=t.Fields[e];else this.CALLBACK_(t)},this.processCharacter_=function(t){if(this.CHAR_++,this.CHAR_IN_LINE_++,"\n"==t&&(this.LINE_++,this.CHAR_IN_LINE_=1),this.SKIPTILLEOL_)return void("\n"==t&&(this.SKIPTILLEOL_=!1));if(this.SKIPCOMMENT_&&"%"==t)return void(this.SKIPTILLEOL_=!0);if(!this.SKIPWS_||!/\s/.test(t)){this.SKIPWS_=!1,this.SKIPCOMMENT_=!1,this.SKIPTILLEOL_=!1;for(var e=!0;e;)switch(e=!1,this.STATE_){case this.STATES_.ENTRY_OR_JUNK:"@"==t&&(this.STATE_=this.STATES_.OBJECT_TYPE,this.DATA_={ObjectType:""}),this.BRACETYPE_=null,this.SKIPWS_=!0,this.SKIPCOMMENT_=!0;break;case this.STATES_.OBJECT_TYPE:if(/[A-Za-z]/.test(t))this.DATA_.ObjectType+=t.toLowerCase(),this.SKIPWS_=!0,this.SKIPCOMMENT_=!0;else{var i=this.DATA_.ObjectType;"comment"==i?this.STATE_=this.STATES_.ENTRY_OR_JUNK:"string"==i?(this.DATA_.ObjectType=i,this.DATA_.Fields={},this.BRACETYPE_=t,this.BRACECOUNT_=1,this.STATE_=this.STATES_.KV_KEY,this.SKIPWS_=!0,this.SKIPCOMMENT_=!0,this.PARSETMP_={Key:""}):"preamble"==i?this.STATE_=this.STATES_.ENTRY_OR_JUNK:i in this.ENTRY_TYPES_?(this.DATA_.ObjectType="entry",this.DATA_.EntryType=i,this.DATA_.EntryKey="",this.STATE_=this.STATES_.ENTRY_KEY,e=!0):(this.error_('Unrecognized object type: "'+this.DATA_.ObjectType+'"'),this.STATE_=this.STATES_.ENTRY_OR_JUNK)}break;case this.STATES_.ENTRY_KEY:if(("{"===t||"("===t)&&null==this.BRACETYPE_){this.BRACETYPE_=t,this.BRACECOUNT_=1,this.SKIPWS_=!0,this.SKIPCOMMENT_=!0;break}/[,%\s]/.test(t)?this.DATA_.EntryKey.length<1?(this.SKIPWS_=!0,this.SKIPCOMMENT_=!0):null==this.BRACETYPE_?(this.error_("No opening brace for object."),this.STATE_=this.STATES_.ENTRY_OR_JUNK):(this.SKIPWS_=!0,this.SKIPCOMMENT_=!0,e=!0,this.STATE_=this.STATES_.KV_KEY,this.PARSETMP_.Key="",this.DATA_.Fields={}):(this.DATA_.EntryKey+=t,this.SKIPWS_=!1,this.SKIPCOMMENT_=!1);break;case this.STATES_.KV_KEY:if("}"==t&&"{"==this.BRACETYPE_||")"==t&&"("==this.BRACETYPE_){this.processEntry_(),this.SKIPWS_=!0,this.SKIPCOMMENT_=!0,this.STATE_=this.STATES_.ENTRY_OR_JUNK;break}/[\-A-Za-z:]/.test(t)?(this.PARSETMP_.Key+=t,this.SKIPWS_=!1,this.SKIPCOMMENT_=!1):this.PARSETMP_.Key.length<1?(this.SKIPWS_=!0,this.SKIPCOMMENT_=!0):(this.SKIPWS_=!0,this.SKIPCOMMENT_=!0,this.STATE_=this.STATES_.EQUALS,e=!0);break;case this.STATES_.EQUALS:if("}"==t&&"{"==this.BRACETYPE_||")"==t&&"("==this.BRACETYPE_){this.error_('Key-value pair has key "'+this.PARSETMP_.Key+'", but no value.'),this.processEntry_(),this.SKIPWS_=!0,this.SKIPCOMMENT_=!0,this.STATE_=this.STATES_.ENTRY_OR_JUNK;break}"="==t&&(this.SKIPWS_=!0,this.SKIPCOMMENT_=!0,this.STATE_=this.STATES_.KV_VALUE,this.PARSETMP_.Value="",this.VALBRACES_={'"':[],"{":[]});break;case this.STATES_.KV_VALUE:var n=this.VALBRACES_,s=this.PARSETMP_.Value,o=!1;if('"'==t||"{"==t||"}"==t||","==t){if(","==t&&0===n['"'].length+n["{"].length){var a=this.PARSETMP_.Value.trim();a in this.MACROS_?this.PARSETMP_.Value=this.MACROS_[a]:this.error_("Reference to an undefined macro: "+a),o=!0}if('"'==t){if(0===n['"'].length+n["{"].length){n['"'].push(this.CHAR_),this.SKIPWS_=!1,this.SKIPCOMMENT_=!1;break}1!=n['"'].length||0!=n["{"].length||0!=s.length&&"\\"==s[s.length-1]||(o=!0)}if("{"==t&&(0==s.length||"\\"!=s[s.length-1])&&(n["{"].push(this.CHAR_),this.SKIPWS_=!1,this.SKIPCOMMENT_=!1),"}"==t)if(0===n['"'].length+n["{"].length){var a=this.PARSETMP_.Value.trim();a in this.MACROS_?this.PARSETMP_.Value=this.MACROS_[a]:this.error_("Reference to an undefined macro: "+a),e=!0,o=!0}else(0==s.length||"\\"!=s[s.length-1])&&n["{"].length>0&&(n["{"].splice(n["{"].length-1,1),0==n["{"].length+n['"'].length&&(o=!0))}o?(this.SKIPWS_=!0,this.SKIPCOMMENT_=!0,this.STATE_=this.STATES_.KV_KEY,this.DATA_.Fields[this.PARSETMP_.Key]=this.PARSETMP_.Value,this.PARSETMP_={Key:""},this.VALBRACES_=null):this.PARSETMP_.Value+=t}}},this.CHARCONV_=[[/\\space /g," 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When writing up your analysis, please manually"," review your histories and find all references"," that should be cited in order to completely describe your work. 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0!==s&&(t.exports=s))}).call(e,i(2))},function(t,e,i){var n,s;(function(o,a,r){n=[i(44),i(33),i(6),i(5)],s=function(t,e,i,n){"use strict";var s=t.FoldoutListItemView,l=t.ListItemView,c=s.extend({className:s.prototype.className+" dataset-collection",id:function(){return["dataset_collection",this.model.get("id")].join("-")},initialize:function(t){this.linkTarget=t.linkTarget||"_blank",this.hasUser=t.hasUser,s.prototype.initialize.call(this,t)},_setUpListeners:function(){s.prototype._setUpListeners.call(this),this.listenTo(this.model,"change",function(t,e){o.isEqual(o.keys(t.changed),["deleted"])&&this.render()})},_renderSubtitle:function(){var t=a('<div class="subtitle"></div>');switch(this.model.get("collection_type")){case"list":return t.text(n("a list of datasets"));case"paired":return t.text(n("a pair of datasets"));case"list:paired":return t.text(n("a list of paired datasets"))}return t},_getFoldoutPanelOptions:function(){var t=s.prototype._getFoldoutPanelOptions.call(this);return o.extend(t,{linkTarget:this.linkTarget,hasUser:this.hasUser})},$selector:function(){return this.$("> .selector")},toString:function(){var t=this.model?this.model+"":"(no model)";return"DCListItemView("+t+")"}});c.prototype.templates=function(){var t=o.extend({},s.prototype.templates.warnings,{error:i.wrapTemplate(["<% if( model.error ){ %>",'<div class="errormessagesmall">',n("There was an error getting the data for this collection"),": <%- model.error %>","</div>","<% } %>"]),purged:i.wrapTemplate(["<% if( model.purged ){ %>",'<div class="purged-msg warningmessagesmall">',n("This collection has been deleted and removed from disk"),"</div>","<% } %>"]),deleted:i.wrapTemplate(["<% if( model.deleted && !model.purged ){ %>",'<div class="deleted-msg warningmessagesmall">',n("This collection has been deleted"),"</div>","<% } %>"])}),e=i.wrapTemplate(['<div class="title-bar clear" tabindex="0">','<div class="title">','<span class="name"><%- collection.element_identifier || collection.name 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dataset-collection-element",initialize:function(t){t.logger&&(this.logger=this.model.logger=t.logger),this.log("DatasetDCEListItemView.initialize:",t),e.DatasetListItemView.prototype.initialize.call(this,t)},_fetchModelDetails:function(){var t=this;return t.model.inReadyState()&&!t.model.hasDetails()?t.model.fetch({silent:!0}):r.when()},toString:function(){var t=this.model?this.model+"":"(no model)";return"DatasetDCEListItemView("+t+")"}});h.prototype.templates=function(){var t=i.wrapTemplate(['<div class="title-bar clear" tabindex="0">','<span class="state-icon"></span>','<div class="title">','<span class="name"><%- element.element_identifier %></span>',"</div>","</div>"],"element");return o.extend({},e.DatasetListItemView.prototype.templates,{titleBar:t})}();var u=c.extend({className:c.prototype.className+" dataset-collection-element",_swapNewRender:function(t){c.prototype._swapNewRender.call(this,t);var e=this.model.get("state")||"ok";return this.$el.addClass("state-"+e),this.$el},toString:function(){var t=this.model?this.model+"":"(no model)";return"NestedDCDCEListItemView("+t+")"}});return{DCListItemView:c,DCEListItemView:d,DatasetDCEListItemView:h,NestedDCDCEListItemView:u}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(3),i(1),i(1))},function(t,e,i){var n,s;(function(o,a,r){n=[i(71),i(6),i(5)],s=function(t,e,i){"use strict";var n="collections",s={defaults:{model_class:"DatasetCollectionElement",element_identifier:null,element_index:null,element_type:null},_mergeObject:function(t){return o.extend(t,t.object,{element_id:t.id}),delete t.object,t},constructor:function(t,e){t=this._mergeObject(t),this.idAttribute="element_id",a.Model.apply(this,arguments)},parse:function(t,e){var i=t;return 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t=a.Model.prototype.toJSON.call(this);return this.elements&&(t.elements=this.elements.toJSON()),t},inReadyState:function(){var t=this.get("populated");return this.isDeletedOrPurged()||t},hasDetails:function(){return this.debug("hasDetails:",this.elements.length),0!==this.elements.length},getVisibleContents:function(t){return this.elements},"delete":function(t){return this.get("deleted")?r.when():this.save({deleted:!0},t)},undelete:function(t){return!this.get("deleted")||this.get("purged")?r.when():this.save({deleted:!1},t)},isDeletedOrPurged:function(){return this.get("deleted")||this.get("purged")},searchAttributes:["name"],toString:function(){var t=[this.get("id"),this.get("name")||this.get("element_identifier")];return"DatasetCollection("+t.join(",")+")"}}),p=u.extend({collectionClass:h,initialize:function(t,e){this.debug(this+"(ListDatasetCollection).initialize:",t,e),u.prototype.initialize.call(this,t,e)},toString:function(){return["ListDatasetCollection(",this.get("name"),")"].join("")}}),g=p.extend({initialize:function(t,e){this.debug(this+"(PairDatasetCollection).initialize:",t,e),p.prototype.initialize.call(this,t,e)},toString:function(){return["PairDatasetCollection(",this.get("name"),")"].join("")}}),f=u.extend(e.mixin(s,{constructor:function(t,e){this.debug(" NestedDCDCE.constructor:",t,e),s.constructor.call(this,t,e)},toString:function(){var t=this.object?""+this.object:this.get("element_identifier");return["NestedDCDCE(",t,")"].join("")}})),m=c.extend({model:f,initialize:function(t,e){this.debug(this+"(NestedDCDCECollection).initialize:",t,e),c.prototype.initialize.call(this,t,e)},toString:function(){return["NestedDCDCECollection(",this.length,")"].join("")}}),v=g.extend(e.mixin(s,{constructor:function(t,e){this.debug(" NestedPairDCDCE.constructor:",t,e),s.constructor.call(this,t,e)},toString:function(){var 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t=this,e=this.$el.parent().width();this.$el.animate({"margin-right":e},"fast",function(){t.trigger("discard",{source:t}),t.destroy()})},destroy:function(){this.off(),this.$el.remove()},events:{click:"_click","click .name":"_clickName","click .discard":"_clickDiscard",dragstart:"_dragstart",dragend:"_dragend",dragover:"_sendToParent",drop:"_sendToParent"},_click:function(t){t.stopPropagation(),this.select(t)},_clickName:function(t){t.stopPropagation(),t.preventDefault();var e=([c("Enter a new name for the element"),":\n(",c("Note that changing the name here will not rename the dataset"),")"].join(""),prompt(c("Enter a new name for the element")+":",this.element.name));e&&(this.element.name=e,this.render())},_clickDiscard:function(t){t.stopPropagation(),this.discard()},_dragstart:function(t){t.originalEvent&&(t=t.originalEvent),t.dataTransfer.effectAllowed="move",t.dataTransfer.setData("text/plain",JSON.stringify(this.element)),this.$el.addClass("dragging"),this.$el.parent().trigger("collection-element.dragstart",[this])},_dragend:function(t){this.$el.removeClass("dragging"),this.$el.parent().trigger("collection-element.dragend",[this])},_sendToParent:function(t){this.$el.parent().trigger(t)},toString:function(){return"DatasetCollectionElementView()"}}),p=o.View.extend(i.LoggableMixin).extend({_logNamespace:h,elementViewClass:u,collectionClass:t.HistoryListDatasetCollection,className:"list-collection-creator collection-creator flex-row-container",minElements:1,defaultAttributes:{creationFn:function(){throw new TypeError("no creation fn for 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dataset"),"</div>"],"dataset"),a[e.DISCARDED]=n.wrapTemplate(["<div>",s("The job creating this dataset was cancelled before completion"),"</div>"],"dataset"),a[e.QUEUED]=n.wrapTemplate(["<div>",s("This job is waiting to run"),"</div>"],"dataset"),a[e.RUNNING]=n.wrapTemplate(["<div>",s("This job is currently running"),"</div>"],"dataset"),a[e.UPLOAD]=n.wrapTemplate(["<div>",s("This dataset is currently uploading"),"</div>"],"dataset"),a[e.SETTING_METADATA]=n.wrapTemplate(["<div>",s("Metadata is being auto-detected"),"</div>"],"dataset"),a[e.PAUSED]=n.wrapTemplate(["<div>",s('This job is paused. Use the "Resume Paused Jobs" in the history menu to resume'),"</div>"],"dataset"),a[e.ERROR]=n.wrapTemplate(["<% if( !dataset.purged ){ %>","<div><%- dataset.misc_blurb %></div>","<% } %>",'<span class="help-text">',s("An error occurred with this dataset"),":</span>",'<div class="job-error-text"><%- dataset.misc_info %></div>'],"dataset"),a[e.EMPTY]=n.wrapTemplate(["<div>",s("No data"),": <i><%- dataset.misc_blurb %></i></div>"],"dataset"),a.unknown=n.wrapTemplate(['<div>Error: unknown dataset state: "<%- dataset.state %>"</div>'],"dataset");var r={resubmitted:n.wrapTemplate(["<% if( model.resubmitted ){ %>",'<div class="resubmitted-msg infomessagesmall">',s("The job creating this dataset has been resubmitted"),"</div>","<% } %>"])},c=n.wrapTemplate(["<% _.each( apps, function( app ){ %>",'<div class="display-application">','<span class="display-application-location"><%- app.label %></span> ','<span class="display-application-links">',"<% _.each( app.links, function( link ){ %>",'<a target="<%- link.target %>" href="<%- link.href %>">',"<% print( _l( link.text ) ); %>","</a> ","<% }); %>","</span>","</div>","<% }); %>"],"apps");return l.extend({},d.prototype.templates,{warnings:t,details:i,noAccess:o,summaries:a,detailMessages:r,displayApplications:c})}(),{DatasetListItemView:h}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(1),i(2),i(1),i(3))},function(t,e,i){var n,s;(function(o,a,r){n=[i(4)],s=function(t){var e=o.Model.extend({initialize:function(t){this.app=t},checksum:function(){var t="",e=this;return this.app.section.$el.find(".section-row").each(function(){var i=a(this).attr("id"),n=e.app.field_list[i];n&&(t+=i+":"+JSON.stringify(n.value&&n.value())+":"+n.collapsed+";")}),t},create:function(){function t(t,e,i){n.flat_dict[t]=e,o[t]=i,n.app.element_list[e]&&n.app.element_list[e].$el.attr("tour_id",t)}function e(s,o){for(var a in o){var r=o[a];if(r.input){var l=r.input,c=s;switch(""!=s&&(c+="|"),c+=l.name,l.type){case"repeat":var d="section-",h=[],u=null;for(var p in r){var g=p.indexOf(d);-1!=g&&(g+=d.length,h.push(parseInt(p.substr(g))),u||(u=p.substr(0,g)))}h.sort(function(t,e){return t-e});var a=0;for(var f in h)e(c+"_"+a++,r[u+h[f]]);break;case"conditional":var m=n.app.field_list[l.id].value();t(c+"|"+l.test_param.name,l.id,m);var v=i(l,m);-1!=v&&e(c,o[l.id+"-section-"+v]);break;case"section":e(!l.flat&&c||"",r);break;default:var _=n.app.field_list[l.id];if(_&&_.value){var m=_.value();if((void 0===l.ignore||l.ignore!=m)&&(_.collapsed&&l.collapsible_value&&(m=l.collapsible_value),t(c,l.id,m),l.payload))for(var y in l.payload)t(y,l.id,l.payload[y])}}}}}var n=this,s={};this._iterate(this.app.section.$el,s);var o={};return this.flat_dict={},e("",s),o},match:function(t){return this.flat_dict&&this.flat_dict[t]},matchCase:function(t,e){return i(t,e)},matchModel:function(t,e){return s(t.inputs,this.flat_dict,e)},matchResponse:function(t){function e(t,s){if("string"==typeof s){var o=n.flat_dict[t];o&&(i[o]=s)}else for(var a in s){var r=a;if(""!==t){var l="|";s instanceof Array&&(l="_"),r=t+l+r}e(r,s[a])}}var i={},n=this;return e("",t),i},_iterate:function(t,e){var i=this,n=a(t).children();n.each(function(){var t=this,n=a(t).attr("id");if(a(t).hasClass("section-row")){var s=i.app.input_list[n];e[n]=s&&{input:s}||{},i._iterate(t,e[n])}else i._iterate(t,e)})}}),i=function(t,e){"boolean"==t.test_param.type&&(e="true"==e?t.test_param.truevalue||"true":t.test_param.falsevalue||"false");for(var i in t.cases)if(t.cases[i].value==e)return i;return-1},n=function(t,e,i,s){s=a.extend(!0,{},s),r.each(t,function(t){t&&t.type&&(s[t.name]=t)}),r.each(t,function(t){r.isObject(t)&&(t.type&&s[t[e]]?i(t,s[t[e]]):n(t,e,i,s))})},s=function(t,e,n){function s(t,o){for(var a in o){var r=o[a],l=r.name;switch(""!=t&&(l=t+"|"+l),r.type){case"repeat":for(var c in r.cache)s(l+"_"+c,r.cache[c]);break;case"conditional":var d=i(r,r.test_param&&r.test_param.value);-1!=d&&s(l,r.cases[d].inputs);break;case"section":s(l,r.inputs);break;default:var h=e[l];h&&n(h,r)}}}var o={};return s("",t),o};return{Manager:e,matchIds:s,matchContext:n}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(1),i(3))},function(t,e,i){var n,s;(function(i){n=[],s=function(){return i.View.extend({initialize:function(t,e){this.app=t,this.field=e.field,this.text_enable=t.options.text_enable||"Enable",this.text_disable=t.options.text_disable||"Disable",this.cls_enable=t.options.cls_enable||"fa fa-caret-square-o-down",this.cls_disable=t.options.cls_disable||"fa fa-caret-square-o-up",this.setElement(this._template(e)),this.$field=this.$(".ui-form-field"),this.$preview=this.$(".ui-form-preview"),this.$collapsible=this.$(".ui-form-collapsible"),this.$collapsible_icon=this.$(".ui-form-collapsible").find(".icon"),this.$error_text=this.$(".ui-form-error-text"),this.$error=this.$(".ui-form-error"),this.$backdrop=this.$(".ui-form-backdrop"),this.$field.prepend(this.field.$el),this.field.collapsed=void 0!==e.collapsible_value&&JSON.stringify(e.value)==JSON.stringify(e.collapsible_value),this._refresh();var i=this;this.$collapsible.on("click",function(){i.field.collapsed=!i.field.collapsed,i._refresh()})},disable:function(t){this.$backdrop.show(),t&&this.$backdrop.css({opacity:0,cursor:"default"})},error:function(t){this.$error_text.html(t),this.$error.show(),this.$el.addClass("ui-error")},reset:function(){this.$error.hide(),this.$el.removeClass("ui-error")},_refresh:function(){this.$collapsible_icon.removeClass().addClass("icon"),this.field.collapsed?(this.$field.hide(),this.$preview.show(),this._tooltip(this.text_enable,this.cls_enable)):(this.$field.fadeIn("fast"),this.$preview.hide(),this._tooltip(this.text_disable,this.cls_disable)),this.app.trigger("change")},_tooltip:function(t,e){this.$collapsible_icon.addClass(e).tooltip({placement:"bottom"}).attr("data-original-title",t).tooltip("fixTitle").tooltip("hide")},_template:function(t){var e='<div class="ui-form-element"><div class="ui-form-error ui-error"><span class="fa fa-arrow-down"/><span class="ui-form-error-text"/></div><div class="ui-form-title">';return e+=t.disabled||void 0===t.collapsible_value?t.label:'<div class="ui-form-collapsible"><i class="icon"/>'+t.label+"</div>",e+='</div><div class="ui-form-field">',e+='<div class="ui-form-info">',t.help&&(e+=t.help,t.argument&&-1==t.help.indexOf("("+t.argument+")")&&(e+=" ("+t.argument+")")),e+='</div><div class="ui-form-backdrop"/></div>',t.collapsible_preview&&(e+='<div class="ui-form-preview">'+t.text_value+"</div>"),e+="</div>"}})}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2))},function(t,e,i){var n,s;(function(o,a){n=[i(4),i(7),i(39),i(52),i(51),i(48)],s=function(t,e,i,n,s,r){return o.Model.extend({types:{text:"_fieldText",select:"_fieldSelect",data_column:"_fieldSelect",genomebuild:"_fieldSelect",data:"_fieldData",data_collection:"_fieldData",integer:"_fieldSlider","float":"_fieldSlider","boolean":"_fieldBoolean",drill_down:"_fieldDrilldown",color:"_fieldColor",hidden:"_fieldHidden",hidden_data:"_fieldHidden",baseurl:"_fieldHidden",library_data:"_fieldLibrary",ftpfile:"_fieldFtp"},initialize:function(t,e){this.app=t},create:function(t){void 0===t.value&&(t.value=null),void 0===t.default_value&&(t.default_value=t.value);var e=null,i=this.types[t.type];return i&&"function"==typeof this[i]&&(e=this[i].call(this,t)),e||(this.app.incompatible=!0,e=t.options?this._fieldSelect(t):this._fieldText(t),Galaxy.emit.debug("form-parameters::_addRow()","Auto matched field type ("+t.type+").")),void 0!==t.value&&e.value(t.value),e},_fieldData:function(t){var e=this;return new i.View(this.app,{id:"field-"+t.id,extensions:t.extensions,optional:t.optional,multiple:t.multiple,type:t.type,data:t.options,onchange:function(){e.app.trigger("change")}})},_fieldSelect:function(t){if(t.is_workflow)return this._fieldText(t);"data_column"==t.type&&(t.error_text="Missing columns in referenced dataset.");var i=[];for(var n in t.options){var s=t.options[n];i.push({label:s[0],value:s[1]})}var o=e.Select;switch(t.display){case"checkboxes":o=e.Checkbox;break;case"radio":o=e.Radio}var a=this;return new o.View({id:"field-"+t.id,data:i,error_text:t.error_text||"No options available",optional:t.optional&&null===t.default_value,multiple:t.multiple,optional:t.optional,searchable:t.searchable,onchange:function(){a.app.trigger("change")}})},_fieldDrilldown:function(t){if(t.is_workflow)return this._fieldText(t);var i=this;return new e.Drilldown.View({id:"field-"+t.id,data:t.options,display:t.display,onchange:function(){i.app.trigger("change")}})},_fieldText:function(i){if(i.options)if(i.area=i.multiple,t.validate(i.value)){if(a.isArray(i.value)){var n="";for(var s in i.value){if(n+=String(i.value[s]),!i.multiple)break;n+="\n"}i.value=n}}else i.value=null;var o=this;return new e.Input({id:"field-"+i.id,area:i.area,onchange:function(t){i.onchange?i.onchange(t):o.app.trigger("change")}})},_fieldSlider:function(t){var i=this;return new e.Slider.View({id:"field-"+t.id,precise:"float"==t.type,is_workflow:t.is_workflow,min:t.min,max:t.max,onchange:function(){i.app.trigger("change")}})},_fieldHidden:function(t){return new e.Hidden({id:"field-"+t.id,info:t.info})},_fieldBoolean:function(t){var i=this;return new e.RadioButton.View({id:"field-"+t.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}],onchange:function(){i.app.trigger("change")}})},_fieldColor:function(t){var e=this;return new r({id:"field-"+t.id,onchange:function(){e.app.trigger("change")}})},_fieldLibrary:function(t){var e=this;return new n.View({id:"field-"+t.id,optional:t.optional,multiple:t.multiple,onchange:function(){e.app.trigger("change")}})},_fieldFtp:function(t){var e=this;return new s.View({id:"field-"+t.id,optional:t.optional,multiple:t.multiple,onchange:function(){e.app.trigger("change")}})}})}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(1))},function(t,e,i){var n,s;(function(o,a,r){n=[i(4),i(14),i(9),i(7)],s=function(t,e,i,n){var s=o.View.extend({initialize:function(i){this.options=t.merge(i,{title:"Section",empty_text:"Not available.",max:null,min:null}),this.setElement("<div/>"),this.button_new=new n.ButtonIcon({icon:"fa-plus",title:"Insert "+this.options.title_new,tooltip:"Add new "+this.options.title_new+" block",floating:"clear",onclick:function(){i.onnew&&i.onnew()}}),this.table=new e.View({cls:"ui-table-plain",content:""}),this.$el.append(this.table.$el),this.$el.append(a("<div/>").append(this.button_new.$el)),this.list={},this.n=0},size:function(){return this.n},add:function(t){if(!t.id||this.list[t.id])return void Galaxy.emit.debug("form-repeat::add()","Duplicate repeat block id.");this.n++;var e=new n.ButtonIcon({icon:"fa-trash-o",tooltip:"Delete this repeat block",cls:"ui-button-icon-plain",onclick:function(){t.ondel&&t.ondel()}}),s=new i.View({id:t.id,title:"placeholder",cls:"ui-portlet-repeat",operations:{button_delete:e}});s.append(t.$el),s.$el.addClass("section-row"),this.list[t.id]=s,this.table.add(s.$el),this.table.append("row_"+t.id,!0),this.options.max>0&&this.n>=this.options.max&&this.button_new.disable(),this._refresh()},del:function(t){if(!this.list[t])return void Galaxy.emit.debug("form-repeat::del()","Invalid repeat block id.");this.n--;var e=this.table.get("row_"+t);e.remove(),delete this.list[t],this.button_new.enable(),this._refresh()},hideOptions:function(){this.button_new.$el.hide(),r.each(this.list,function(t){t.hideOperation("button_delete")}),r.isEmpty(this.list)&&this.$el.append(a("<div/>").addClass("ui-form-info").html(this.options.empty_text))},_refresh:function(){var t=0;for(var e in this.list){var i=this.list[e];i.title(++t+": "+this.options.title),this.n>this.options.min?i.showOperation("button_delete"):i.hideOperation("button_delete")}}});return{View:s}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(1),i(3))},function(t,e,i){var n,s;(function(o,a,r,l){n=[i(4),i(14),i(7),i(9),i(37),i(35),i(36)],s=function(t,e,i,n,s,c,d){var h=o.View.extend({initialize:function(t,i){this.app=t,this.inputs=i.inputs,i.cls="ui-table-plain",i.cls_tr="section-row",this.table=new e.View(i),this.parameters=new d(t,i),this.setElement(this.table.$el),this.render()},render:function(){this.table.delAll();for(var t in this.inputs)this.add(this.inputs[t])},add:function(e){var i=a.extend(!0,{},e);i.id=e.id=t.uid(),this.app.input_list[i.id]=i;var n=i.type;switch(n){case"conditional":this._addConditional(i);break;case"repeat":this._addRepeat(i);break;case"section":this._addSection(i);break;default:this._addRow(i)}},_addConditional:function(t){var e=this;t.test_param.id=t.id,this.app.options.sustain_conditionals&&(t.test_param.disabled=!0);var i=this._addRow(t.test_param);i.options.onchange=function(i){var n=e.app.data.matchCase(t,i);for(var s in t.cases){var o=t.cases[s],a=t.id+"-section-"+s,r=e.table.get(a),l=!1;for(var c in o.inputs)if(!o.inputs[c].hidden){l=!0;break}s==n&&l?r.fadeIn("fast"):r.hide()}e.app.trigger("change")};for(var n in t.cases){var s=t.id+"-section-"+n,o=new h(this.app,{inputs:t.cases[n].inputs});o.$el.addClass("ui-table-section"),this.table.add(o.$el),this.table.append(s)}i.trigger("change")},_addRepeat:function(t){function e(e){var s=t.id+"-section-"+n++,a=new h(i.app,{inputs:e});o.add({id:s,$el:a.$el,ondel:function(){o.del(s),i.app.trigger("change")}})}for(var i=this,n=0,o=new s.View({title:t.title||"Repeat",title_new:t.title||"",min:t.min,max:t.max,onnew:function(){e(t.inputs),i.app.trigger("change")}}),a=t.min,l=r.size(t.cache),d=0;d<Math.max(l,a);d++){var u=null;u=l>d?t.cache[d]:t.inputs,e(u)}this.app.options.sustain_repeats&&o.hideOptions();var p=new c(this.app,{label:t.title||t.name,help:t.help,field:o});this.table.add(p.$el),this.table.append(t.id)},_addSection:function(t){var e=this,s=new h(e.app,{inputs:t.inputs}),o=new i.ButtonIcon({icon:"fa-eye-slash",tooltip:"Show/hide section",cls:"ui-button-icon-plain"}),a=new n.View({title:t.title||t.name,cls:"ui-portlet-section",collapsible:!0,collapsed:!0,operations:{button_visible:o}});a.append(s.$el),a.append(l("<div/>").addClass("ui-form-info").html(t.help)),a.setOperation("button_visible",function(){a.collapsed?a.expand():a.collapse()}),a.on("expanded",function(){o.setIcon("fa-eye")}),a.on("collapsed",function(){o.setIcon("fa-eye-slash")}),this.app.on("expand",function(t){a.$("#"+t).length>0&&a.expand()}),t.expanded&&a.expand(),this.table.add(a.$el),this.table.append(t.id)},_addRow:function(t){var e=t.id,i=this.parameters.create(t);this.app.field_list[e]=i;var n=new c(this.app,{name:t.name,label:t.label||t.name,value:t.value,default_value:t.default_value,text_value:t.text_value||t.value,collapsible_value:t.collapsible_value,collapsible_preview:t.collapsible_preview,help:t.help,argument:t.argument,disabled:t.disabled,field:i});return this.app.element_list[e]=n,this.table.add(n.$el),this.table.append(e),t.hidden&&this.table.get(e).hide(),i}});return{View:h}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(1),i(3),i(1))},function(t,e,i){var n,s;(function(o,a,r){n=[i(4),i(7),i(27)],s=function(t,e,i){var n=o.View.extend({initialize:function(i,n){this.app=i,this.options=n,this.history={};var s=this;this.setElement('<div class="ui-select-content"/>'),this.list={};var o=[];"data_collection"==n.type?this.mode="collection":n.multiple?this.mode="multiple":this.mode="single",this.current=this.mode,this.list={};var l=t.textify(n.extensions),c="No dataset available.";l&&(c="No "+l+" dataset available.");var d="No dataset list available.";if(l&&(d="No "+l+" dataset collection available."),"single"==this.mode&&(o.push({icon:"fa-file-o",value:"single",tooltip:"Single dataset"}),this.select_single=new e.Select.View({optional:n.optional,error_text:c,onchange:function(){s.trigger("change")}}),this.list.single={field:this.select_single,type:"hda"}),("single"==this.mode||"multiple"==this.mode)&&(o.push({icon:"fa-files-o",value:"multiple",tooltip:"Multiple datasets"}),this.select_multiple=new e.Select.View({multiple:!0,searchable:!1,optional:n.optional,error_text:c,onchange:function(){s.trigger("change")}}),this.list.multiple={field:this.select_multiple,type:"hda"}),"single"==this.mode||"multiple"==this.mode||"collection"==this.mode){o.push({icon:"fa-folder-o",value:"collection",tooltip:"Dataset collection"});var h="multiple"==this.mode;this.select_collection=new e.Select.View({error_text:d,multiple:h,searchable:!1,optional:n.optional,onchange:function(){s.trigger("change")}}),this.list.collection={field:this.select_collection,type:"hdca"}}this.button_type=new e.RadioButton.View({value:this.current,data:o,onchange:function(t){s.current=t,s.refresh(),s.trigger("change")}}),this.$batch=a(this.template_batch());var u=r.size(this.list),p=0;u>1&&(this.$el.append(this.button_type.$el),p=Math.max(0,35*r.size(this.list))+"px");for(var g in this.list)this.$el.append(this.list[g].field.$el.css({"margin-left":p}));this.$el.append(this.$batch.css({"margin-left":p})),this.update(n.data),void 0!==this.options.value&&this.value(this.options.value),this.refresh(),this.on("change",function(){n.onchange&&n.onchange(s.value())})},wait:function(){for(var t in this.list)this.list[t].field.wait()},unwait:function(){for(var t in this.list)this.list[t].field.unwait()},update:function(t){function e(t,e){if(t){var n=[];for(var s in e){var o=e[s];n.push({hid:o.hid,label:o.hid+": "+o.name,value:o.id}),i.history[o.id+"_"+o.src]=o}t.add(n,function(t,e){return e.hid-t.hid})}}var i=this;e(this.select_single,t.hda),e(this.select_multiple,t.hda),e(this.select_collection,t.hdca)},value:function(t){if(void 0!==t)if(t&&t.values)try{var e=[];for(var i in t.values)e.push(t.values[i].id);t&&t.values.length>0&&"hdca"==t.values[0].src?(this.current="collection",this.select_collection.value(e)):"multiple"==this.mode?(this.current="multiple",this.select_multiple.value(e)):(this.current="single",this.select_single.value(e[0]))}catch(n){Galaxy.emit.debug("tools-select-content::value()","Skipped.")}else for(var i in this.list)this.list[i].field.value(null);this.refresh();var s=this._select().value();if(null===s)return null;if(s instanceof Array||(s=[s]),0===s.length)return null;var o={batch:this._batch(),values:[]};for(var i in s){var a=this.history[s[i]+"_"+this.list[this.current].type];if(!a)return null;o.values.push(a)}return o.values.sort(function(t,e){return t.hid-e.hid}),o},refresh:function(){this.button_type.value(this.current);for(var t in this.list){var e=this.list[t].field.$el;this.current==t?e.show():e.hide()}this._batch()?this.$batch.show():this.$batch.hide()},_select:function(){return this.list[this.current].field},_batch:function(){if("collection"==this.current){var t=this.history[this._select().value()+"_hdca"];if(t&&t.map_over_type)return!0}return"single"!=this.current&&"single"==this.mode?!0:!1},template_batch:function(){return'<div class="ui-form-info"><i class="fa fa-sitemap" style="font-size: 1.2em; padding: 2px 5px;"/>This is a batch mode input field. A separate job will be triggered for each dataset.</div>'}});return{View:n}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(1),i(3))},function(t,e,i){var n,s;(function(o,a,r){n=[i(4),i(9),i(7),i(38),i(34)],s=function(t,e,i,n,s){return o.View.extend({initialize:function(e){this.options=t.merge(e,{initial_errors:!1,cls:"ui-portlet-limited",icon:""}),this.modal=parent.Galaxy&&parent.Galaxy.modal||new i.Modal.View,this.setElement("<div/>"),this.render()},update:function(t){var e=this;this.data.matchModel(t,function(t,i){var n=e.input_list[t];if(n&&n.options&&!a.isEqual(n.options,i.options)){n.options=i.options;var s=e.field_list[t];if(s.update){var o=[];if(-1!=["data","data_collection","drill_down"].indexOf(n.type))o=n.options;else for(var r in i.options){var l=i.options[r];l.length>2&&o.push({label:l[0],value:l[1]})}s.update(o),s.trigger("change"),Galaxy.emit.debug("form-view::update()","Updating options for "+t)}}})},wait:function(t){for(var e in this.input_list){var i=this.field_list[e],n=this.input_list[e];n.is_dynamic&&i.wait&&i.unwait&&(t?i.wait():i.unwait())}},highlight:function(t,e,i){var n=this.element_list[t];if(n&&(n.error(e||"Please verify this parameter."),this.trigger("expand",t),!i))if(self==top){var s=this.$el.parents().filter(function(){return"auto"==r(this).css("overflow")}).first();s.animate({scrollTop:s.scrollTop()+n.$el.offset().top-50},500)}else r("html, body").animate({scrollTop:n.$el.offset().top-20},500)},errors:function(t){if(this.trigger("reset"),t&&t.errors){var e=this.data.matchResponse(t.errors);for(var i in this.element_list){this.element_list[i];e[i]&&this.highlight(i,e[i],!0)}}},render:function(){var t=this;this.off("change"),this.off("reset"),this.field_list={},this.input_list={},this.element_list={},this.data=new s.Manager(this),this._renderForm(),this.data.create(),this.options.initial_errors&&this.errors(this.options);var e=this.data.checksum();return this.on("change",function(){var i=t.data.checksum();i!=e&&(e=i,t.options.onchange&&t.options.onchange())}),this.on("reset",function(){for(var t in this.element_list)this.element_list[t].reset()}),this},_renderForm:function(){this.message=new i.Message,this.section=new n.View(this,{inputs:this.options.inputs}),r(".tooltip").remove(),this.portlet=new e.View({icon:this.options.icon,title:this.options.title,cls:this.options.cls,operations:this.options.operations,buttons:this.options.buttons,collapsible:this.options.collapsible,collapsed:this.options.collapsed}),this.portlet.append(this.message.$el),this.portlet.append(this.section.$el),this.$el.empty(),this.$el.append(this.portlet.$el),this.options.message&&this.message.update({persistent:!0,status:"warning",message:this.options.message}),Galaxy.emit.debug("form-view::initialize()","Completed")}})}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(3),i(1))},function(t,e,i){var n,s;(function(o){n=[i(31),i(42),i(5)],s=function(t,e,i){"use strict";function n(t){return function(e,i){return this.isNew()&&(i=i||{},i.url=this.urlRoot+this.get("history_id")+"/contents",e=e||{},e.type="dataset_collection"),t.call(this,e,i)}}var s=e.HistoryContentMixin,a=t.ListDatasetCollection,r=t.PairDatasetCollection,l=t.ListPairedDatasetCollection,c=a.extend(s).extend({defaults:o.extend(o.clone(a.prototype.defaults),{history_content_type:"dataset_collection",collection_type:"list",model_class:"HistoryDatasetCollectionAssociation"}),initialize:function(t,e){a.prototype.initialize.call(this,t,e),s.initialize.call(this,t,e)},save:n(a.prototype.save),toString:function(){return["HistoryListDatasetCollection(",this.get("name"),")"].join("")}}),d=r.extend(s).extend({defaults:o.extend(o.clone(r.prototype.defaults),{history_content_type:"dataset_collection",collection_type:"paired",model_class:"HistoryDatasetCollectionAssociation"}),initialize:function(t,e){r.prototype.initialize.call(this,t,e),s.initialize.call(this,t,e)},save:n(r.prototype.save),toString:function(){return["HistoryPairDatasetCollection(",this.get("name"),")"].join("")}}),h=l.extend(s).extend({defaults:o.extend(o.clone(l.prototype.defaults),{history_content_type:"dataset_collection",collection_type:"list:paired",model_class:"HistoryDatasetCollectionAssociation"}),initialize:function(t,e){l.prototype.initialize.call(this,t,e),s.initialize.call(this,t,e)},save:n(l.prototype.save),toString:function(){return["HistoryListPairedDatasetCollection(",this.get("name"),")"].join("")}});return{HistoryListDatasetCollection:c,HistoryPairDatasetCollection:d,HistoryListPairedDatasetCollection:h}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(3))},function(t,e,i){var n,s;(function(o,a){n=[i(12),i(6),i(5)],s=function(t,e,i){"use strict";var n="history",s=function(t,e){return[t,e].join("-")},r={defaults:{history_id:null,history_content_type:null,hid:null,visible:!0},idAttribute:"type_id",constructor:function(t,e){t.type_id=s(t.history_content_type,t.id),this.debug("HistoryContentMixin.constructor:",t.type_id),o.Model.apply(this,arguments)},_typeIdStr:function(){return s(this.get("history_content_type"),this.get("id"))},initialize:function(t,e){this.on("change:id",this._createTypeId)},_createTypeId:function(){this.set("type_id",this._typeIdStr())},isNew:function(){return!this.get("id")},hidden:function(){return!this.get("visible")},isVisible:function(t,e){var i=!0;return t||!this.get("deleted")&&!this.get("purged")||(i=!1),e||this.get("visible")||(i=!1),i},urlRoot:Galaxy.root+"api/histories/",url:function(){var t=this.urlRoot+this.get("history_id")+"/contents/"+this.get("history_content_type")+"s/"+this.get("id");return t},hide:function(t){return this.get("visible")?this.save({visible:!1},t):a.when()},unhide:function(t){return this.get("visible")?a.when():this.save({visible:!0},t)},toString:function(){var t=this.get("id")||"";return this.get("name")&&(t=this.get("hid")+' :"'+this.get("name")+'",'+t),"HistoryContent("+t+")"}},l=o.Model.extend(e.LoggableMixin).extend(r).extend({_logNamespace:n
});return{typeIdStr:s,HistoryContentMixin:r,HistoryContent:l}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(1))},function(t,e,i){var n,s;(function(o,a,r){n=[i(42),i(73),i(41),i(6),i(5)],s=function(t,e,i,n,s){"use strict";var l="history",c=o.Collection.extend(n.LoggableMixin).extend({_logNamespace:l,model:function(t,n){if("dataset"===t.history_content_type)return new e.HistoryDatasetAssociation(t,n);if("dataset_collection"===t.history_content_type){switch(t.collection_type){case"list":return new i.HistoryListDatasetCollection(t,n);case"paired":return new i.HistoryPairDatasetCollection(t,n);case"list:paired":return new i.HistoryListPairedDatasetCollection(t,n)}return{validationError:"Unknown collection_type: "+t.history_content_type}}return{validationError:"Unknown history_content_type: "+t.history_content_type}},initialize:function(t,e){e=e||{},this.historyId=e.historyId,this.model.prototype.idAttribute="type_id",this.on("all",function(){this.debug(this+".event:",arguments)})},urlRoot:Galaxy.root+"api/histories",url:function(){return this.urlRoot+"/"+this.historyId+"/contents"},ids:function(){return this.map(function(t){return t.get("id")})},notReady:function(){return this.filter(function(t){return!t.inReadyState()})},running:function(){var t=[];return this.each(function(e){var i=!e.inReadyState();i&&t.push(e.get("id"))}),t},getByHid:function(t){return a.first(this.filter(function(e){return e.get("hid")===t}))},getVisible:function(t,e,i){i=i||[],this.debug("checking isVisible");var n=new c(this.filter(function(i){return i.isVisible(t,e)}));return a.each(i,function(t){a.isFunction(t)&&(n=new c(n.filter(t)))}),n},hidden:function(){function t(t){return t.hidden()}return new c(this.filter(t))},deleted:function(){function t(t){return t.get("deleted")}return new c(this.filter(t))},haveDetails:function(){return this.all(function(t){return t.hasDetails()})},fetchAllDetails:function(t){t=t||{};var e={details:"all"};return t.data=t.data?a.extend(t.data,e):e,this.fetch(t)},ajaxQueue:function(t,e){var i=r.Deferred(),n=this.length,s=[];if(!n)return i.resolve([]),i;var o=this.chain().reverse().map(function(a,r){return function(){var l=t.call(a,e);l.done(function(t){i.notify({curr:r,total:n,response:t,model:a})}),l.always(function(t){s.push(t),o.length?o.shift()():i.resolve(s)})}}).value();return o.shift()(),i},isCopyable:function(t){var e=["HistoryDatasetAssociation","HistoryDatasetCollectionAssociation"];return a.isObject(t)&&t.id&&a.contains(e,t.model_class)},copy:function(t){var e,i,n;a.isString(t)?(e=t,n="hda",i="dataset"):(e=t.id,n={HistoryDatasetAssociation:"hda",LibraryDatasetDatasetAssociation:"ldda",HistoryDatasetCollectionAssociation:"hdca"}[t.model_class]||"hda",i="hdca"===n?"dataset_collection":"dataset");var s=this,o=r.post(this.url(),{content:e,source:n,type:i}).done(function(t){s.add([t])}).fail(function(t,a,r){s.trigger("error",s,o,{},"Error copying contents",{type:i,id:e,source:n})});return o},matches:function(t){return this.filter(function(e){return e.matches(t)})},set:function(e,i){e=a.isArray(e)?e:[e],a.each(e,function(e){e.type_id&&e.get&&e.get("type_id")||(e.type_id=t.typeIdStr(e.history_content_type,e.id))}),o.Collection.prototype.set.call(this,e,i)},createHDCA:function(t,e,n,s){var o=this,a={list:i.HistoryListDatasetCollection,paired:i.HistoryPairDatasetCollection},r=new a[e]({history_id:this.historyId,name:n,element_identifiers:t});return r.save().done(function(t){o.add(r)}).fail(function(t,e,i){o.trigger("error",t,e,i)})},clone:function(){var t=o.Collection.prototype.clone.call(this);return t.historyId=this.historyId,t},print:function(){var t=this;t.each(function(e){t.debug(e),e.elements&&t.debug(" elements:",e.elements)})},toString:function(){return["HistoryContents(",[this.historyId,this.length].join(),")"].join("")}});return{HistoryContents:c}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(3),i(1))},function(t,e,i){var n,s;(function(o,a,r,l){n=[i(6),i(5)],s=function(t,e){"use strict";var i="list",n=o.View.extend(t.LoggableMixin).extend({_logNamespace:i,initialize:function(t){this.expanded=t.expanded||!1,this.log(" expanded:",this.expanded),this.fxSpeed=void 0!==t.fxSpeed?t.fxSpeed:this.fxSpeed},fxSpeed:"fast",render:function(t){var e=this._buildNewRender();return this._setUpBehaviors(e),this._queueNewRender(e,t),this},_buildNewRender:function(){var t=a(this.templates.el(this.model.toJSON(),this));return this.expanded&&this.$details(t).replaceWith(this._renderDetails().show()),t},_queueNewRender:function(t,e){e=void 0===e?this.fxSpeed:e;var i=this;a(i).queue("fx",[function(t){this.$el.fadeOut(e,t)},function(e){i._swapNewRender(t),e()},function(t){this.$el.fadeIn(e,t)},function(t){this.trigger("rendered",i),t()}])},_swapNewRender:function(t){return this.$el.empty().attr("class",r.isFunction(this.className)?this.className():this.className).append(t.children())},_setUpBehaviors:function(t){t=t||this.$el,t.find("[title]").tooltip({placement:"bottom"})},$details:function(t){return t=t||this.$el,t.find("> .details")},_renderDetails:function(){var t=a(this.templates.details(this.model.toJSON(),this));return this._setUpBehaviors(t),t},toggleExpanded:function(t){return t=void 0===t?!this.expanded:t,t?this.expand():this.collapse(),this},expand:function(){var t=this;return t._fetchModelDetails().always(function(){t._expand()})},_fetchModelDetails:function(){return this.model.hasDetails()?l.when():this.model.fetch()},_expand:function(){var t=this,e=t._renderDetails();t.$details().replaceWith(e),t.expanded=!0,t.$details().slideDown({duration:t.fxSpeed,step:function(){t.trigger("expanding",t)},complete:function(){t.trigger("expanded",t)}})},collapse:function(){this.debug(this+"(ExpandableView).collapse");var t=this;t.expanded=!1,this.$details().slideUp({duration:t.fxSpeed,step:function(){t.trigger("collapsing",t)},complete:function(){t.trigger("collapsed",t)}})}}),s=n.extend(t.mixin(t.SelectableViewMixin,t.DraggableViewMixin,{tagName:"div",className:"list-item",initialize:function(e){n.prototype.initialize.call(this,e),t.SelectableViewMixin.initialize.call(this,e),t.DraggableViewMixin.initialize.call(this,e),this._setUpListeners()},_setUpListeners:function(){return this.on("selectable",function(t){t?this.$(".primary-actions").hide():this.$(".primary-actions").show()},this),this},_buildNewRender:function(){var t=n.prototype._buildNewRender.call(this);return t.children(".warnings").replaceWith(this._renderWarnings()),t.children(".title-bar").replaceWith(this._renderTitleBar()),t.children(".primary-actions").append(this._renderPrimaryActions()),t.find("> .title-bar .subtitle").replaceWith(this._renderSubtitle()),t},_swapNewRender:function(t){return n.prototype._swapNewRender.call(this,t),this.selectable&&this.showSelector(0),this.draggable&&this.draggableOn(),this.$el},_renderWarnings:function(){var t=this,e=a('<div class="warnings"></div>'),i=t.model.toJSON();return r.each(t.templates.warnings,function(n){e.append(a(n(i,t)))}),e},_renderTitleBar:function(){return a(this.templates.titleBar(this.model.toJSON(),this))},_renderPrimaryActions:function(){return[]},_renderSubtitle:function(){return a(this.templates.subtitle(this.model.toJSON(),this))},events:{"click .title-bar":"_clickTitleBar","keydown .title-bar":"_keyDownTitleBar","click .selector":"toggleSelect"},_clickTitleBar:function(t){t.stopPropagation(),t.altKey?(this.toggleSelect(t),this.selectable||this.showSelector()):this.toggleExpanded()},_keyDownTitleBar:function(t){var e=32,i=13;return!t||"keydown"!==t.type||t.keyCode!==e&&t.keyCode!==i?!0:(this.toggleExpanded(),t.stopPropagation(),!1)},toString:function(){var t=this.model?this.model+"":"(no model)";return"ListItemView("+t+")"}}));s.prototype.templates=function(){var e=t.wrapTemplate(['<div class="list-element">','<div class="warnings"></div>','<div class="selector">','<span class="fa fa-2x fa-square-o"></span>',"</div>",'<div class="primary-actions"></div>','<div class="title-bar"></div>','<div class="details"></div>',"</div>"]),i={},n=t.wrapTemplate(['<div class="title-bar clear" tabindex="0">','<span class="state-icon"></span>','<div class="title">','<span class="name"><%- element.name %></span>',"</div>",'<div class="subtitle"></div>',"</div>"],"element"),s=t.wrapTemplate(['<div class="subtitle"></div>']),o=t.wrapTemplate(['<div class="details"></div>']);return{el:e,warnings:i,titleBar:n,subtitle:s,details:o}}();var c=s.extend({foldoutStyle:"foldout",foldoutPanelClass:null,initialize:function(t){"drilldown"===this.foldoutStyle&&(this.expanded=!1),this.foldoutStyle=t.foldoutStyle||this.foldoutStyle,this.foldoutPanelClass=t.foldoutPanelClass||this.foldoutPanelClass,s.prototype.initialize.call(this,t),this.foldout=this._createFoldoutPanel()},_renderDetails:function(){if("drilldown"===this.foldoutStyle)return a();var t=s.prototype._renderDetails.call(this);return this._attachFoldout(this.foldout,t)},_createFoldoutPanel:function(){var t=this.model,e=this._getFoldoutPanelClass(t),i=this._getFoldoutPanelOptions(t),n=new e(r.extend(i,{model:t}));return n},_getFoldoutPanelClass:function(){return this.foldoutPanelClass},_getFoldoutPanelOptions:function(){return{foldoutStyle:this.foldoutStyle,fxSpeed:this.fxSpeed}},_attachFoldout:function(t,e){return e=e||this.$("> .details"),this.foldout=t.render(0),t.$("> .controls").hide(),e.append(t.$el)},expand:function(){var t=this;return t._fetchModelDetails().always(function(){"foldout"===t.foldoutStyle?t._expand():"drilldown"===t.foldoutStyle&&t._expandByDrilldown()})},_expandByDrilldown:function(){var t=this;t.listenTo(t.foldout,"close",function(){t.trigger("collapsed:drilldown",t,t.foldout)}),t.trigger("expanded:drilldown",t,t.foldout)}});return c.prototype.templates=function(){var e=t.wrapTemplate(['<div class="details">',"</div>"],"collection");return r.extend({},s.prototype.templates,{details:e})}(),{ExpandableView:n,ListItemView:s,FoldoutListItemView:c}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(1),i(3),i(1))},function(t,e,i){var n,s;(function(o){n=[i(4),i(56),i(7),i(40),i(20),i(18),i(29)],s=function(t,e,i,n,s,a,r){return n.extend({initialize:function(t){var i=this;n.prototype.initialize.call(this,t),this.deferred=new e,t.inputs?(this._buildForm(t),t.needs_update&&this.deferred.execute(function(t){i._updateModel(t)})):this.deferred.execute(function(e){i._buildModel(e,t,!0)})},remove:function(){var t=this;this.$el.hide(),this.deferred.execute(function(){n.prototype.remove.call(t),Galaxy.emit.debug("tool-form-base::remove()","Destroy view.")})},_buildForm:function(e){var i=this;this.options=t.merge(e,this.options),this.options=t.merge({icon:void 0===e.icon&&"fa-wrench"||"",title:"<b>"+e.name+"</b> "+e.description+" (Galaxy Version "+e.version+")",operations:this._operations(),onchange:function(){i.deferred.reset(),i.deferred.execute(function(t){i._updateModel(t)})}},this.options),this.options.customize&&this.options.customize(this.options),this.render(),this.options.collapsible||this.$el.append(o("<div/>").addClass("ui-margin-top-large").append(this._footer()))},_buildModel:function(e,n,s){var a=this;this.options.id=n.id,this.options.version=n.version;var r="",l={};n.job_id?r=Galaxy.root+"api/jobs/"+n.job_id+"/build_for_rerun":(r=Galaxy.root+"api/tools/"+n.id+"/build",Galaxy.params&&Galaxy.params.tool_id==n.id&&(l=o.extend({},Galaxy.params),n.version&&(l.tool_version=n.version))),t.request({type:"GET",url:r,data:l,success:function(t){a._buildForm(t.tool_model||t),!s&&a.message.update({status:"success",message:"Now you are using '"+a.options.name+"' version "+a.options.version+", id '"+a.options.id+"'.",persistent:!1}),Galaxy.emit.debug("tool-form-base::initialize()","Initial tool model ready.",t),e.resolve()},error:function(t){var n=t&&t.err_msg||"Uncaught error.";a.$el.is(":empty")?a.$el.prepend(new i.Message({message:n,status:"danger",persistent:!0,large:!0}).$el):Galaxy.modal.show({title:"Tool request failed",body:n,buttons:{Close:function(){Galaxy.modal.hide()}}}),Galaxy.emit.debug("tool-form::initialize()","Initial tool model request failed.",t),e.reject()}})},_updateModel:function(e){var i=this,n=this.options.update_url||Galaxy.root+"api/tools/"+this.options.id+"/build",s={tool_id:this.options.id,tool_version:this.options.version,inputs:o.extend(!0,{},i.data.create())};this.wait(!0),Galaxy.emit.debug("tool-form-base::_updateModel()","Sending current state.",s),t.request({type:"POST",url:n,data:s,success:function(t){i.update(t.tool_model||t),i.options.update&&i.options.update(t),i.wait(!1),Galaxy.emit.debug("tool-form-base::_updateModel()","Received new model.",t),e.resolve()},error:function(t){Galaxy.emit.debug("tool-form-base::_updateModel()","Refresh request failed.",t),e.reject()}})},_operations:function(){var t=this,e=this.options,n=new i.ButtonMenu({icon:"fa-cubes",title:!e.narrow&&"Versions"||null,tooltip:"Select another tool version"});if(!e.sustain_version&&e.versions&&e.versions.length>1)for(var o in e.versions){var a=e.versions[o];a!=e.version&&n.addMenu({title:"Switch to "+a,version:a,icon:"fa-cube",onclick:function(){var i=e.id.replace(e.version,this.version),n=this.version;t.deferred.reset(),t.deferred.execute(function(e){t._buildModel(e,{id:i,version:n})})}})}else n.$el.hide();var r=new i.ButtonMenu({icon:"fa-caret-down",title:!e.narrow&&"Options"||null,tooltip:"View available options"});return e.biostar_url&&(r.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(e.biostar_url+"/p/new/post/")}}),r.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(e.biostar_url+"/local/search/page/?q="+e.name)}})),r.addMenu({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",window.location.origin+Galaxy.root+"root?tool_id="+e.id)}}),Galaxy.user&&Galaxy.user.get("is_admin")&&r.addMenu({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=Galaxy.root+"api/tools/"+e.id+"/download"}}),e.requirements&&e.requirements.length>0&&r.addMenu({icon:"fa-info-circle",title:"Requirements",tooltip:"Display tool requirements",onclick:function(){this.visible?(this.visible=!1,t.message.update({message:""})):(this.visible=!0,t.message.update({persistent:!0,message:s.requirements(e),status:"info"}))}}),e.sharable_url&&r.addMenu({icon:"fa-external-link",title:"See in Tool Shed",tooltip:"Access the repository",onclick:function(){window.open(e.sharable_url)}}),{menu:r,versions:n}},_footer:function(){var t=this.options,e=o("<div/>").append(s.help(t));if(t.citations){var i=o("<div/>"),n=new a.ToolCitationCollection;n.tool_id=t.id;var l=new r.CitationListView({el:i,collection:n});l.render(),n.fetch(),e.append(i)}return e}})}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(1))},function(t,e,i){var n,s;(function(o,a){n=[i(3),i(17),i(11),i(19)],s=function(t,e,i,n){"use strict";var s={hidden:!1,show:function(){this.set("hidden",!1)},hide:function(){this.set("hidden",!0)},toggle:function(){this.set("hidden",!this.get("hidden"))},is_visible:function(){return!this.attributes.hidden}},r=o.Model.extend({defaults:{name:null,label:null,type:null,value:null,html:null,num_samples:5},initialize:function(t){this.attributes.html=unescape(this.attributes.html)},copy:function(){return new r(this.toJSON())},set_value:function(t){this.set("value",t||"")}}),l=o.Collection.extend({model:r}),c=r.extend({}),d=r.extend({set_value:function(t){this.set("value",parseInt(t,10))},get_samples:function(){return d3.scale.linear().domain([this.get("min"),this.get("max")]).ticks(this.get("num_samples"))}}),h=d.extend({set_value:function(t){this.set("value",parseFloat(t))}}),u=r.extend({get_samples:function(){return t.map(this.get("options"),function(t){return t[0]})}});r.subModelTypes={integer:d,"float":h,data:c,select:u};var p=o.Model.extend({defaults:{id:null,name:null,description:null,target:null,inputs:[],outputs:[]},urlRoot:Galaxy.root+"api/tools",initialize:function(e){this.set("inputs",new l(t.map(e.inputs,function(t){var e=r.subModelTypes[t.type]||r;return new e(t)})))},toJSON:function(){var t=o.Model.prototype.toJSON.call(this);return t.inputs=this.get("inputs").map(function(t){return t.toJSON()}),t},remove_inputs:function(t){var e=this,i=e.get("inputs").filter(function(e){return-1!==t.indexOf(e.get("type"))});e.get("inputs").remove(i)},copy:function(t){var e=new p(this.toJSON());if(t){var i=new o.Collection;e.get("inputs").each(function(t){t.get_samples()&&i.push(t)}),e.set("inputs",i)}return e},apply_search_results:function(e){return-1!==t.indexOf(e,this.attributes.id)?this.show():this.hide(),this.is_visible()},set_input_value:function(t,e){this.get("inputs").find(function(e){return e.get("name")===t}).set("value",e)},set_input_values:function(e){var i=this;t.each(t.keys(e),function(t){i.set_input_value(t,e[t])})},run:function(){return this._run()},rerun:function(t,e){return this._run({action:"rerun",target_dataset_id:t.id,regions:e})},get_inputs_dict:function(){var t={};return this.get("inputs").each(function(e){t[e.get("name")]=e.get("value")}),t},_run:function(n){var s=t.extend({tool_id:this.id,inputs:this.get_inputs_dict()},n),o=a.Deferred(),r=new e.ServerStateDeferred({ajax_settings:{url:this.urlRoot,data:JSON.stringify(s),dataType:"json",contentType:"application/json",type:"POST"},interval:2e3,success_fn:function(t){return"pending"!==t}});return a.when(r.go()).then(function(t){o.resolve(new i.DatasetCollection(t))}),o}});t.extend(p.prototype,s);var g=(o.View.extend({}),o.Collection.extend({model:p})),f=o.Model.extend(s),m=o.Model.extend({defaults:{elems:[],open:!1},clear_search_results:function(){t.each(this.attributes.elems,function(t){t.show()}),this.show(),this.set("open",!1)},apply_search_results:function(e){var i,n=!0;t.each(this.attributes.elems,function(t){t instanceof f?(i=t,i.hide()):t instanceof p&&t.apply_search_results(e)&&(n=!1,i&&i.show())}),n?this.hide():(this.show(),this.set("open",!0))}});t.extend(m.prototype,s);var v=o.Model.extend({defaults:{search_hint_string:"search tools",min_chars_for_search:3,clear_btn_url:"",search_url:"",visible:!0,query:"",results:null,clear_key:27},urlRoot:Galaxy.root+"api/tools",initialize:function(){this.on("change:query",this.do_search)},do_search:function(){var t=this.attributes.query;if(t.length<this.attributes.min_chars_for_search)return void this.set("results",null);var e=t;this.timer&&clearTimeout(this.timer),a("#search-clear-btn").hide(),a("#search-spinner").show();var i=this;this.timer=setTimeout(function(){"undefined"!=typeof ga&&ga("send","pageview",Galaxy.root+"?q="+e),a.get(i.urlRoot,{q:e},function(t){i.set("results",t),a("#search-spinner").hide(),a("#search-clear-btn").show()},"json")},400)},clear_search:function(){this.set("query",""),this.set("results",null)}});t.extend(v.prototype,s);var _=o.Model.extend({initialize:function(t){this.attributes.tool_search=t.tool_search,this.attributes.tool_search.on("change:results",this.apply_search_results,this),this.attributes.tools=t.tools,this.attributes.layout=new o.Collection(this.parse(t.layout))},parse:function(e){var i=this,n=function(e){var s=e.model_class;if(s.indexOf("Tool")===s.length-4)return i.attributes.tools.get(e.id);if("ToolSection"===s){var o=t.map(e.elems,n);return e.elems=o,new m(e)}return"ToolSectionLabel"===s?new f(e):void 0};return t.map(e,n)},clear_search_results:function(){this.get("layout").each(function(t){t instanceof m?t.clear_search_results():t.show()})},apply_search_results:function(){var t=this.get("tool_search").get("results");if(null===t)return void this.clear_search_results();var e=null;this.get("layout").each(function(i){i instanceof f?(e=i,e.hide()):i instanceof p?i.apply_search_results(t)&&e&&e.show():(e=null,i.apply_search_results(t))})}}),y=o.View.extend({initialize:function(){this.model.on("change:hidden",this.update_visible,this),this.update_visible()},update_visible:function(){this.model.attributes.hidden?this.$el.hide():this.$el.show()}}),w=y.extend({tagName:"div",render:function(){var t=a("<div/>");if(t.append(S.tool_link(this.model.toJSON())),"upload1"===this.model.id)t.find("a").on("click",function(t){t.preventDefault(),Galaxy.upload.show()});else if("Tool"===this.model.get("model_class")){var e=this;t.find("a").on("click",function(t){t.preventDefault();var i=new n.View({id:e.model.id,version:e.model.get("version")});i.deferred.execute(function(){Galaxy.app.display(i)})})}return this.$el.append(t),this}}),b=y.extend({tagName:"div",className:"toolPanelLabel",render:function(){return this.$el.append(a("<span/>").text(this.model.attributes.text)),this}}),x=y.extend({tagName:"div",className:"toolSectionWrapper",initialize:function(){y.prototype.initialize.call(this),this.model.on("change:open",this.update_open,this)},render:function(){this.$el.append(S.panel_section(this.model.toJSON()));var e=this.$el.find(".toolSectionBody");return t.each(this.model.attributes.elems,function(t){if(t instanceof p){var i=new w({model:t,className:"toolTitle"});i.render(),e.append(i.$el)}else if(t instanceof f){var n=new b({model:t});n.render(),e.append(n.$el)}}),this},events:{"click .toolSectionTitle > 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this.model.set("query",this.$el.find(":input").val())}}),$=o.View.extend({tagName:"div",className:"toolMenu",initialize:function(){this.model.get("tool_search").on("change:results",this.handle_search_results,this)},render:function(){var t=this,e=new C({model:this.model.get("tool_search")});return e.render(),t.$el.append(e.$el),this.model.get("layout").each(function(e){if(e instanceof m){var i=new x({model:e});i.render(),t.$el.append(i.$el)}else if(e instanceof p){var n=new w({model:e,className:"toolTitleNoSection"});n.render(),t.$el.append(n.$el)}else if(e instanceof f){var s=new b({model:e});s.render(),t.$el.append(s.$el)}}),t.$el.find("a.tool-link").click(function(e){var i=a(this).attr("class").split(/\s+/)[0],n=t.model.get("tools").get(i);t.trigger("tool_link_click",e,n)}),this},handle_search_results:function(){var t=this.model.get("tool_search").get("results");t&&0===t.length?a("#search-no-results").show():a("#search-no-results").hide()}}),E=o.View.extend({className:"toolForm",render:function(){this.$el.children().remove(),this.$el.append(S.tool_form(this.model.toJSON()))}}),S=(o.View.extend({className:"toolMenuAndView",initialize:function(){this.tool_panel_view=new $({collection:this.collection}),this.tool_form_view=new E},render:function(){this.tool_panel_view.render(),this.tool_panel_view.$el.css("float","left"),this.$el.append(this.tool_panel_view.$el),this.tool_form_view.$el.hide(),this.$el.append(this.tool_form_view.$el);var t=this;this.tool_panel_view.on("tool_link_click",function(e,i){e.preventDefault(),t.show_tool(i)})},show_tool:function(t){var e=this;t.fetch().done(function(){e.tool_form_view.model=t,e.tool_form_view.render(),e.tool_form_view.$el.show(),a("#left").width("650px")})}}),{tool_search:t.template(['<input id="tool-search-query" class="search-query parent-width" name="query" 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_.each( tool.inputs, function( input ){ %>",'<div class="form-row">','<label for="<%- input.name %>"><%- input.label %>:</label>','<div class="form-row-input">',"<%= input.html %>","</div>",'<div class="toolParamHelp" style="clear: both;">',"<%- input.help %>","</div>",'<div style="clear: both;"></div>',"</div>","<% }); %>","</div>",'<div class="form-row form-actions">','<input type="submit" class="btn btn-primary" name="runtool_btn" value="Execute" />',"</div>",'<div class="toolHelp">','<div class="toolHelpBody"><% tool.help %></div>',"</div>"].join(""),{variable:"tool"})});return{ToolParameter:r,IntegerToolParameter:d,SelectToolParameter:u,Tool:p,ToolCollection:g,ToolSearch:v,ToolPanel:_,ToolPanelView:$,ToolFormView:E}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(1))},function(t,e,i){var n,s;(function(i,o,a,r){n=[],s=function(){var t=i.View.extend({initialize:function(t,e){this.$button=t,this.$button.size()||(this.$button=o("<div/>")),this.options=e||[],this.$button.data("popupmenu",this);var i=this;this.$button.click(function(t){return o(".popmenu-wrapper").remove(),i._renderAndShow(t),!1})},_renderAndShow:function(t){this.render(),this.$el.appendTo("body").css(this._getShownPosition(t)).show(),this._setUpCloseBehavior()},render:function(){if(this.$el.addClass("popmenu-wrapper").hide().css({position:"absolute"}).html(this.template(this.$button.attr("id"),this.options)),this.options.length){var t=this;this.$el.find("li").each(function(e,i){var n=t.options[e];n.func&&o(this).children("a.popupmenu-option").click(function(e){n.func.call(t,e,n),e.preventDefault()})})}return this},template:function(t,e){return['<ul id="',t,'-menu" class="dropdown-menu">',this._templateOptions(e),"</ul>"].join("")},_templateOptions:function(t){return t.length?a.map(t,function(t){if(t.divider)return'<li 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a=s.attr("href"),r=s.attr("target"),l=s.attr("confirm");n.func=function(){if(!l||confirm(l))switch(r){case"_parent":window.parent.location=a;break;case"_top":window.top.location=a;break;default:window.location=a}}}i.push(n)}),i},t.fromExistingDom=function(e,i,n){e=o(e),i=o(i);var s=t.convertLinksToOptions(i,n);return i.remove(),new t(e,s)},t.make_popup_menus=function(e,i,n){e=e||document,i=i||"div[popupmenu]",n=n||function(t,e){return"#"+t.attr("popupmenu")};var s=[];return o(e).find(i).each(function(){var i=o(this),a=o(e).find(n(i,e));s.push(t.fromDom(a,i)),a.addClass("popup")}),s},t}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(1),i(3),i(1))},function(t,e,i){var n,s;(function(o,a){n=[i(4)],s=function(t){return o.View.extend({colors:{standard:["c00000","ff0000","ffc000","ffff00","92d050","00b050","00b0f0","0070c0","002060","7030a0"],base:["ffffff","000000","eeece1","1f497d","4f81bd","c0504d","9bbb59","8064a2","4bacc6","f79646"],theme:[["f2f2f2","7f7f7f","ddd9c3","c6d9f0","dbe5f1","f2dcdb","ebf1dd","e5e0ec","dbeef3","fdeada"],["d8d8d8","595959","c4bd97","8db3e2","b8cce4","e5b9b7","d7e3bc","ccc1d9","b7dde8","fbd5b5"],["bfbfbf","3f3f3f","938953","548dd4","95b3d7","d99694","c3d69b","b2a2c7","92cddc","fac08f"],["a5a5a5","262626","494429","17365d","366092","953734","76923c","5f497a","31859b","e36c09"],["7f7f7e","0c0c0c","1d1b10","0f243e","244061","632423","4f6128","3f3151","205867","974806"]]},initialize:function(e){this.options=t.merge(e,{}),this.setElement(this._template()),this.$panel=this.$(".ui-color-picker-panel"),this.$view=this.$(".ui-color-picker-view"),this.$value=this.$(".ui-color-picker-value"),this.$header=this.$(".ui-color-picker-header"),this._build(),this.visible=!1,this.value(this.options.value),this.$boxes=this.$(".ui-color-picker-box");var i=this;this.$boxes.on("click",function(){i.value(a(this).css("background-color")),i.$header.trigger("click")}),this.$header.on("click",function(){i.visible=!i.visible,i.visible?i.$view.fadeIn("fast"):i.$view.fadeOut("fast")})},value:function(t){return void 0!==t&&null!==t&&(this.$value.css("background-color",t),this.$(".ui-color-picker-box").empty(),this.$(this._getValue()).html(this._templateCheck()),this.options.onchange&&this.options.onchange(t)),this._getValue()},_getValue:function(){function t(t){return("0"+parseInt(t).toString(16)).slice(-2)}var e=this.$value.css("background-color");return e=e.match(/^rgb\((\d+),\s*(\d+),\s*(\d+)\)$/),e?"#"+t(e[1])+t(e[2])+t(e[3]):null},_build:function(){this._content({label:"Theme Colors",colors:this.colors.base,padding:10});for(var t in this.colors.theme){var e={};0==t?e.bottom=!0:t!=this.colors.theme.length-1?(e.top=!0,e.bottom=!0):(e.top=!0,e.padding=5),e.colors=this.colors.theme[t],this._content(e)}this._content({label:"Standard 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return'<div class="ui-color-picker-check fa fa-check"/>'},_templateContent:function(){return'<div class="ui-color-picker-content"><div class="label"/><div class="line"/></div>'},_templateBox:function(t){return'<div id="'+t+'" class="ui-color-picker-box" style="background-color: #'+t+';"/>'},_template:function(){return'<div class="ui-color-picker"><div class="ui-color-picker-header"><div class="ui-color-picker-value"/><div class="ui-color-picker-label">Select a color</div></div><div class="ui-color-picker-view ui-input"><div class="ui-color-picker-panel"/></div>'}})}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(1))},function(t,e,n){var s,o;(function(a){s=[n(4),n(22)],o=function(t,e){var n=e.BaseIcons.extend({initialize:function(t){t.type=t.display||"checkbox",t.multiple="checkbox"==t.display,e.BaseIcons.prototype.initialize.call(this,t),this.initial=!0},value:function(t){var i=e.BaseIcons.prototype.value.call(this,t);if(this.initial&&null!==i&&this.header_index){this.initial=!1;var n=i;a.isArray(n)||(n=[n]);for(var s in n){var o=this.header_index[n[s]];for(var r in o)this._setState(o[r],!0)}}return i},_setState:function(t,e){var i=this.$(".button-"+t),n=this.$(".subgroup-"+t);i.data("is_expanded",e),e?(n.fadeIn("fast"),i.removeClass("fa-plus-square"),i.addClass("fa-minus-square")):(n.hide(),i.removeClass("fa-minus-square"),i.addClass("fa-plus-square"))},_templateOptions:function(e){function n(t,e){var i=t.find(".button-"+e);i.on("click",function(){o._setState(e,!i.data("is_expanded"))})}function s(e,r,l){l=l||[];for(i in r){var c=r[i],d=c.options.length>0,h=l.slice(0);o.header_index[c.value]=h.slice(0);var u=a("<div/>");if(d){var p=t.uid(),g=a('<span class="button-'+p+' ui-drilldown-button fa fa-plus-square"/>'),f=a('<div class="subgroup-'+p+'" style="display: none; margin-left: 25px;"/>');h.push(p);var m=a("<div/>");m.append(g),m.append(o._templateOption({label:c.name,value:c.value})),u.append(m),s(f,c.options,h),u.append(f),n(u,p)}else u.append(o._templateOption({label:c.name,value:c.value}));e.append(u)}}var o=this;this.header_index={};var r=a("<div/>");return s(r,e),r},_template:function(t){return'<div class="ui-options-list drilldown-container" id="'+t.id+'"/>'}});return{View:n}}.apply(e,s),!(void 0!==o&&(t.exports=o))}).call(e,n(1))},function(t,e,i){var n,s;(function(o,a,r){n=[i(4),i(13)],s=function(t,e){var i=o.View.extend({optionsDefault:{id:t.uid(),cls:"ui-select",error_text:"No options available",empty_text:"Nothing selected",visible:!0,wait:!1,multiple:!1,searchable:!0,optional:!1},initialize:function(i){var n=this;this.model=new o.Model,this.options=t.merge(i,this.optionsDefault),this.setElement(this._template(this.options)),this.$select=this.$el.find(".select"),this.$icon_dropdown=this.$el.find(".icon-dropdown"),this.$icon_dropdown.on("click",function(){n.$select.select2&&n.$select.select2("open")});var s=null;this.$(".icon-resize").on("mousedown",function(t){var e=t.pageY,i=n.$select.height();s=s||i,a("#dd-helper").show().on("mousemove",function(t){n.$select.height(Math.max(i+(t.pageY-e),s))}).on("mouseup mouseleave",function(){a("#dd-helper").hide().off()})}),this.options.multiple&&(this.options.searchable?(this.all_button=new e.ButtonCheck({onclick:function(){var t=[];0!==n.all_button.value()&&(t=n._availableOptions()),n.value(t),n.trigger("change")}}),this.$el.prepend(this.all_button.$el)):this.$el.addClass("ui-select-multiple"),this.$select.prop("multiple",!0),this.$icon_dropdown.remove()),this.update(this.options.data),void 0!==this.options.value&&this.value(this.options.value),this.options.visible||this.hide(),this.options.wait?this.wait():this.show(),this.$select.on("change",function(){n.trigger("change")}),this.on("change",function(){n.options.onchange&&n.options.onchange(this.value())})},value:function(t){void 0!==t&&(null===t&&(t="__null__"),(this.exists(t)||this.options.multiple)&&(this.$select.val(t),this.$select.select2&&this.$select.select2("val",t)));var e=this._getValue();return this.all_button&&this.all_button.value(a.isArray(e)&&e.length||0,this._size()),e},first:function(){var t=this.$select.find("option").first();return t.length>0?t.val():null},text:function(){return this.$select.find("option:selected").text()},show:function(){this.unwait(),this.$select.show(),this.$el.show()},hide:function(){this.$el.hide()},wait:function(){this.$icon_dropdown.removeClass(),this.$icon_dropdown.addClass("icon-dropdown fa fa-spinner fa-spin")},unwait:function(){this.$icon_dropdown.removeClass(),this.$icon_dropdown.addClass("icon-dropdown fa fa-caret-down")},disabled:function(){return this.$select.is(":disabled")},enable:function(){this.$select.prop("disabled",!1)},disable:function(){this.$select.prop("disabled",!0)},add:function(t,e){r.each(this.model.get("options"),function(e){!r.findWhere(t,e)&&t.push(e)}),e&&t.sort(e),this.update(t)},update:function(t){var e=this._getValue();this.$select.find("option").remove(),!this.options.multiple&&this.options.optional&&this.$select.append(this._templateOption({value:"__null__",label:this.options.empty_text})),this.model.set("options",t);for(var i in t)this.$select.append(this._templateOption(t[i]));0==this._size()?(this.disable(),this.$select.append(this._templateOption({value:"__null__",label:this.options.error_text}))):this.enable(),this.options.searchable&&(this.$select.select2("destroy"),this.$select.select2({closeOnSelect:!this.options.multiple}),this.$(".select2-container .select2-search input").off("blur")),this.value(e),null!==this._getValue()||this.options.multiple&&this.options.optional||this.value(this.first())},setOnChange:function(t){this.options.onchange=t},exists:function(t){return this.$select.find('option[value="'+t+'"]').length>0},_getValue:function(){var e=this.$select.val();return t.validate(e)?e:null},_availableOptions:function(){var t=[];return this.$select.find("option").each(function(e,i){t.push(a(i).attr("value"))}),t},_size:function(){return this.$select.find("option").length},_templateOption:function(t){return'<option value="'+t.value+'">'+r.escape(t.label)+"</option>"},_template:function(t){return'<div id="'+t.id+'" class="'+t.cls+'"><select id="'+t.id+'_select" class="select"/><div class="icon-dropdown"/><div class="icon-resize"><i class="fa fa-angle-double-right fa-rotate-45"/></div></div>'}});return{View:i}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(1),i(3))},function(t,e,i){var n,s;(function(o){n=[i(4),i(21)],s=function(t,e){var i=o.View.extend({initialize:function(i){var n=this;this.ftpfile_list=new e.View({name:"file",optional:i.optional,multiple:i.multiple,onchange:function(){i.onchange&&i.onchange(n.value())}}),this.setElement(this.ftpfile_list.$el),t.get({url:Galaxy.root+"api/remote_files",success:function(t){var e=[];for(var i in t)e.push({value:t[i].path,label:t[i].path});n.ftpfile_list.update(e)}})},value:function(t){return this.ftpfile_list.value(t)}});return{View:i}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2))},function(t,e,i){var n,s;(function(o){n=[i(4),i(7),i(14),i(21)],s=function(t,e,i,n){var s=o.Collection.extend({url:Galaxy.root+"api/libraries?deleted=false"}),a=o.Collection.extend({initialize:function(){var t=this;this.config=new o.Model({library_id:null}),this.config.on("change",function(){t.fetch({reset:!0})})},url:function(){return Galaxy.root+"api/libraries/"+this.config.get("library_id")+"/contents"}}),r=o.View.extend({initialize:function(t){var i=this;this.libraries=new s,this.datasets=new a,this.options=t,this.library_select=new e.Select.View({onchange:function(t){i.datasets.config.set("library_id",t)}}),this.dataset_list=new n.View({name:"dataset",optional:t.optional,multiple:t.multiple,onchange:function(){i.trigger("change")}}),this.libraries.on("reset",function(){var t=[];i.libraries.each(function(e){t.push({value:e.id,label:e.get("name")})}),i.library_select.update(t)}),this.datasets.on("reset",function(){var t=[],e=i.library_select.text();null!==e&&i.datasets.each(function(e){"file"===e.get("type")&&t.push({value:e.id,label:e.get("name")})}),i.dataset_list.update(t)}),this.on("change",function(){t.onchange&&t.onchange(i.value())}),this.setElement(this._template()),this.$(".library-select").append(this.library_select.$el),this.$el.append(this.dataset_list.$el),this.libraries.fetch({reset:!0,success:function(){i.library_select.trigger("change"),void 0!==i.options.value&&i.value(i.options.value)}})},value:function(t){return this.dataset_list.value(t)},_template:function(){return'<div class="ui-select-library"><div class="library ui-margin-bottom"><span class="library-title">Select Library</span><span class="library-select"/></div></div>'}});return{View:r}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2))},function(t,e,i){var n,s;(function(o,a){n=[i(4)],s=function(t){var e=o.View.extend({initialize:function(e){var i=this;this.options=t.merge(e,{id:t.uid(),min:null,max:null,step:null,precise:!1,split:1e4}),this.setElement(this._template(this.options)),this.useslider=null!==this.options.max&&null!==this.options.min&&this.options.max>this.options.min,null===this.options.step&&(this.options.step=1,this.options.precise&&this.useslider&&(this.options.step=(this.options.max-this.options.min)/this.options.split)),this.useslider?(this.$slider=this.$("#slider"),this.$slider.slider(this.options),this.$slider.on("slide",function(t,e){i.value(e.value)})):this.$(".ui-form-slider-text").css("width","100%"),this.$text=this.$("#text"),void 0!==this.options.value&&this.value(this.options.value);var n=[];this.$text.on("change",function(){i.value(a(this).val())}),this.$text.on("keyup",function(t){n[t.which]=!1,i.options.onchange&&i.options.onchange(a(this).val())}),this.$text.on("keydown",function(t){var e=t.which;n[e]=!0,i.options.is_workflow&&n[16]&&52==e?(i.value("$"),event.preventDefault()):8==e||9==e||13==e||37==e||39==e||e>=48&&57>=e&&!n[16]||e>=96&&105>=e||(190==e||110==e)&&-1==a(this).val().indexOf(".")&&i.options.precise||(189==e||109==e)&&-1==a(this).val().indexOf("-")||i._isParameter(a(this).val())||n[91]||n[17]||event.preventDefault()})},value:function(t){return void 0!==t&&(null===t||""===t||this._isParameter(t)||(isNaN(t)&&(t=0),null!==this.options.max&&(t=Math.min(t,this.options.max)),null!==this.options.min&&(t=Math.max(t,this.options.min))),this.$slider&&this.$slider.slider("value",t),this.$text.val(t),this.options.onchange&&this.options.onchange(t)),this.$text.val()},_isParameter:function(t){return this.options.is_workflow&&"$"===String(t).substring(0,1)},_template:function(t){return'<div id="'+t.id+'" class="ui-form-slider"><input id="text" type="text" class="ui-form-slider-text"/><div id="slider" class="ui-form-slider-element"/></div>'}});return{View:e}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(1))},function(t,e,i){var n,s;(function(i){n=[],s=function(){var t=i.Model.extend({defaults:{extension:"auto",genome:"?",url_paste:"",status:"init",info:null,file_name:"",file_mode:"",file_size:0,file_type:null,file_path:"",file_data:null,percentage:0,space_to_tab:!1,to_posix_lines:!0,enabled:!0},reset:function(t){this.clear().set(this.defaults).set(t)}}),e=i.Collection.extend({model:t});return{Model:t,Collection:e}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2))},,function(t,e,i){var n,s;(function(o,a){n=[i(4)],s=function(t){return o.Model.extend({initialize:function(){this.active={},this.last=null},execute:function(e){var i=this,n=t.uid(),s=e.length>0;this.active[n]=!0;var o=a.Deferred();o.promise().always(function(){delete i.active[n],s&&Galaxy.emit.debug("deferred::execute()",this.state().charAt(0).toUpperCase()+this.state().slice(1)+" "+n)}),a.when(this.last).always(function(){i.active[n]?(s&&Galaxy.emit.debug("deferred::execute()","Running "+n),e(o),!s&&o.resolve()):o.reject()}),this.last=o.promise()},reset:function(){Galaxy.emit.debug("deferred::execute()","Reset");for(var t in this.active)this.active[t]=!1},ready:function(){return a.isEmptyObject(this.active)}})}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(1))},,,,,,,,,,,,function(t,e,i){var n,s;(function(o,a){n=[i(6),i(5),i(16)],s=function(t,e){var i=o.View.extend(t.LoggableMixin).extend(t.HiddenUntilActivatedViewMixin).extend({tagName:"div",className:"annotation-display",initialize:function(t){t=t||{},this.tooltipConfig=t.tooltipConfig||{placement:"bottom"},this.listenTo(this.model,"change:annotation",function(){this.render()}),this.hiddenUntilActivated(t.$activator,t)},render:function(){var t=this;return this.$el.html(this._template()),this.$el.find("[title]").tooltip(this.tooltipConfig),this.$annotation().make_text_editable({use_textarea:!0,on_finish:function(e){t.$annotation().text(e),t.model.save({annotation:e},{silent:!0}).fail(function(){t.$annotation().text(t.model.previous("annotation"))})}}),this},_template:function(){var t=this.model.get("annotation");return['<label class="prompt">',e("Annotation"),"</label>",'<div class="annotation" title="',e("Edit annotation"),'">',a.escape(t),"</div>"].join("")},$annotation:function(){return this.$el.find(".annotation")},remove:function(){this.$annotation.off(),this.stopListening(this.model),o.View.prototype.remove.call(this)},toString:function(){return["AnnotationEditor(",this.model+"",")"].join("")}});return{AnnotationEditor:i}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(3))},function(t,e,i){var n,s;(function(o){n=[i(76),i(31),i(30),i(6),i(5)],s=function(t,e,i,n,s){"use strict";var a="collections",r=t.ModelListPanel,l=r.extend({_logNamespace:a,className:r.prototype.className+" dataset-collection-panel",DatasetDCEViewClass:i.DatasetDCEListItemView,NestedDCDCEViewClass:i.NestedDCDCEListItemView,modelCollectionKey:"elements",initialize:function(t){r.prototype.initialize.call(this,t),this.linkTarget=t.linkTarget||"_blank",this.hasUser=t.hasUser,this.panelStack=[],this.parentName=t.parentName,this.foldoutStyle=t.foldoutStyle||"foldout"},_filterCollection:function(){return this.model.getVisibleContents()},_getItemViewClass:function(t){switch(t.get("element_type")){case"hda":return this.DatasetDCEViewClass;case"dataset_collection":return this.NestedDCDCEViewClass}throw new TypeError("Unknown element type:",t.get("element_type"))},_getItemViewOptions:function(t){var e=r.prototype._getItemViewOptions.call(this,t);return o.extend(e,{linkTarget:this.linkTarget,hasUser:this.hasUser,foldoutStyle:this.foldoutStyle})},_setUpItemViewListeners:function(t){var e=this;return r.prototype._setUpItemViewListeners.call(e,t),e.listenTo(t,{"expanded:drilldown":function(t,e){this._expandDrilldownPanel(e)},"collapsed:drilldown":function(t,e){this._collapseDrilldownPanel(e)}}),this},_expandDrilldownPanel:function(t){this.panelStack.push(t),this.$("> .controls").add(this.$list()).hide(),t.parentName=this.model.get("name"),this.$el.append(t.render().$el)},_collapseDrilldownPanel:function(t){this.panelStack.pop(),this.render()},events:{"click .navigation .back":"close"},close:function(t){this.$el.remove(),this.trigger("close")},toString:function(){return"CollectionView("+(this.model?this.model.get("name"):"")+")"}});l.prototype.templates=function(){var t=n.wrapTemplate(['<div class="controls">','<div class="navigation">','<a class="back" href="javascript:void(0)">','<span class="fa fa-icon fa-angle-left"></span>',s("Back to "),"<%- view.parentName %>","</a>","</div>",'<div class="title">','<div class="name"><%- collection.name || collection.element_identifier %></div>','<div class="subtitle">','<% if( collection.collection_type === "list" ){ %>',s("a list of datasets"),'<% } else if( collection.collection_type === "paired" ){ %>',s("a pair of datasets"),'<% } else if( collection.collection_type === "list:paired" ){ %>',s("a list of paired datasets"),"<% } %>","</div>","</div>","</div>"],"collection");return o.extend(o.clone(r.prototype.templates),{controls:t})}();var c=l.extend({DatasetDCEViewClass:i.DatasetDCEListItemView,toString:function(){return"ListCollectionView("+(this.model?this.model.get("name"):"")+")"}}),d=c.extend({toString:function(){return"PairCollectionView("+(this.model?this.model.get("name"):"")+")"}}),h=l.extend({NestedDCDCEViewClass:i.NestedDCDCEListItemView.extend({foldoutPanelClass:d}),toString:function(){return"ListOfPairsCollectionView("+(this.model?this.model.get("name"):"")+")"}});return{CollectionView:l,ListCollectionView:c,PairCollectionView:d,ListOfPairsCollectionView:h}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(3))},function(t,e,i){var n,s;(function(o,a){n=[i(12),i(33),i(77),i(68),i(23),i(6),i(5)],s=function(t,e,n,s,r,l,c){"use strict";var d=e.DatasetListItemView,h=d.extend({initialize:function(t){d.prototype.initialize.call(this,t),this.hasUser=t.hasUser,this.purgeAllowed=t.purgeAllowed||!1,this.tagsEditorShown=t.tagsEditorShown||!1,this.annotationEditorShown=t.annotationEditorShown||!1},_renderPrimaryActions:function(){var e=d.prototype._renderPrimaryActions.call(this);return this.model.get("state")===t.NOT_VIEWABLE?e:d.prototype._renderPrimaryActions.call(this).concat([this._renderEditButton(),this._renderDeleteButton()])},_renderEditButton:function(){if(this.model.get("state")===t.DISCARDED||!this.model.get("accessible"))return null;var e=this.model.get("purged"),i=this.model.get("deleted"),n={title:c("Edit attributes"),href:this.model.urls.edit,target:this.linkTarget,faIcon:"fa-pencil",classes:"edit-btn"};return i||e?(n.disabled=!0,e?n.title=c("Cannot edit attributes of datasets removed from disk"):i&&(n.title=c("Undelete dataset to edit attributes"))):o.contains([t.UPLOAD,t.NEW],this.model.get("state"))&&(n.disabled=!0,n.title=c("This dataset is not yet editable")),r(n)},_renderDeleteButton:function(){if(!this.model.get("accessible"))return null;var t=this,e=this.model.isDeletedOrPurged();return r({title:c(e?"Dataset is already deleted":"Delete"),disabled:e,faIcon:"fa-times",classes:"delete-btn",onclick:function(){t.$el.find(".icon-btn.delete-btn").trigger("mouseout"),t.model["delete"]()}})},_renderDetails:function(){var e=d.prototype._renderDetails.call(this),i=this.model.get("state");return!this.model.isDeletedOrPurged()&&o.contains([t.OK,t.FAILED_METADATA],i)&&(this._renderTags(e),this._renderAnnotation(e),this._makeDbkeyEditLink(e)),this._setUpBehaviors(e),e},_renderSecondaryActions:function(){var e=d.prototype._renderSecondaryActions.call(this);switch(this.model.get("state")){case t.UPLOAD:case t.NEW:case t.NOT_VIEWABLE:return e;case t.ERROR:return e.unshift(this._renderErrButton()),e.concat([this._renderRerunButton()]);case t.OK:case t.FAILED_METADATA:return e.concat([this._renderRerunButton(),this._renderVisualizationsButton()])}return e.concat([this._renderRerunButton()])},_renderErrButton:function(){return r({title:c("View or report this error"),href:this.model.urls.report_error,classes:"report-error-btn",target:this.linkTarget,faIcon:"fa-bug"})},_renderRerunButton:function(){var t=this.model.get("creating_job");return this.model.get("rerunnable")?r({title:c("Run this job again"),href:this.model.urls.rerun,classes:"rerun-btn",target:this.linkTarget,faIcon:"fa-refresh",onclick:function(e){e.preventDefault(),!function(){var e=[i(19)];(function(e){var i=new e.View({job_id:t});i.deferred.execute(function(){Galaxy.app.display(i)})}).apply(null,e)}()}}):void 0},_renderVisualizationsButton:function(){var t=this.model.get("visualizations");if(this.model.isDeletedOrPurged()||!this.hasUser||!this.model.hasData()||o.isEmpty(t))return null;if(!o.isObject(t[0]))return this.warn("Visualizations have been switched off"),null;var e=a(this.templates.visualizations(t,this));return e.find('[target="galaxy_main"]').attr("target",this.linkTarget),this._addScratchBookFn(e.find(".visualization-link").addBack(".visualization-link")),e},_addScratchBookFn:function(t){t.click(function(t){Galaxy.frame&&Galaxy.frame.active&&(Galaxy.frame.add({title:"Visualization",url:a(this).attr("href")}),t.preventDefault(),t.stopPropagation())})},_renderTags:function(t){if(this.hasUser){var e=this;this.tagsEditor=new n.TagsEditor({model:this.model,el:t.find(".tags-display"),onshowFirstTime:function(){this.render()},onshow:function(){e.tagsEditorShown=!0},onhide:function(){e.tagsEditorShown=!1},$activator:r({title:c("Edit dataset tags"),classes:"tag-btn",faIcon:"fa-tags"}).appendTo(t.find(".actions .right"))}),this.tagsEditorShown&&this.tagsEditor.toggle(!0)}},_renderAnnotation:function(t){if(this.hasUser){var e=this;this.annotationEditor=new s.AnnotationEditor({model:this.model,el:t.find(".annotation-display"),onshowFirstTime:function(){this.render()},onshow:function(){e.annotationEditorShown=!0},onhide:function(){e.annotationEditorShown=!1},$activator:r({title:c("Edit dataset annotation"),classes:"annotate-btn",faIcon:"fa-comment"}).appendTo(t.find(".actions .right"))}),this.annotationEditorShown&&this.annotationEditor.toggle(!0)}},_makeDbkeyEditLink:function(t){if("?"===this.model.get("metadata_dbkey")&&!this.model.isDeletedOrPurged()){var e=a('<a class="value">?</a>').attr("href",this.model.urls.edit).attr("target",this.linkTarget);t.find(".dbkey .value").replaceWith(e)}},events:o.extend(o.clone(d.prototype.events),{"click .undelete-link":"_clickUndeleteLink","click .purge-link":"_clickPurgeLink","click .edit-btn":function(t){this.trigger("edit",this,t)},"click .delete-btn":function(t){this.trigger("delete",this,t)},"click .rerun-btn":function(t){this.trigger("rerun",this,t)},"click .report-err-btn":function(t){this.trigger("report-err",this,t)},"click .visualization-btn":function(t){this.trigger("visualize",this,t)},"click .dbkey a":function(t){this.trigger("edit",this,t)}}),_clickUndeleteLink:function(t){return this.model.undelete(),!1},_clickPurgeLink:function(t){return this.model.purge(),!1},toString:function(){var t=this.model?this.model+"":"(no model)";return"HDAEditView("+t+")"}});return h.prototype.templates=function(){var t=o.extend({},d.prototype.templates.warnings,{failed_metadata:l.wrapTemplate(['<% if( dataset.state === "failed_metadata" ){ %>','<div class="failed_metadata-warning warningmessagesmall">',c("An error occurred setting the metadata for this dataset"),'<br /><a href="<%- dataset.urls.edit %>" target="<%- view.linkTarget %>">',c("Set it manually or retry auto-detection"),"</a>","</div>","<% } %>"],"dataset"),deleted:l.wrapTemplate(["<% if( dataset.deleted && !dataset.purged ){ %>",'<div class="deleted-msg warningmessagesmall">',c("This dataset has been deleted"),'<br /><a class="undelete-link" href="javascript:void(0);">',c("Undelete it"),"</a>","<% if( view.purgeAllowed ){ %>",'<br /><a class="purge-link" href="javascript:void(0);">',c("Permanently remove it from disk"),"</a>","<% } %>","</div>","<% } %>"],"dataset")}),e=l.wrapTemplate(["<% if( visualizations.length === 1 ){ %>",'<a class="visualization-btn visualization-link icon-btn" href="<%- visualizations[0].href %>"',' target="<%- visualizations[0].target %>" title="',c("Visualize in"),' <%- visualizations[0].html %>">','<span class="fa fa-bar-chart-o"></span>',"</a>","<% } else { %>",'<div class="visualizations-dropdown dropdown">','<a class="visualization-btn icon-btn" data-toggle="dropdown" title="',c("Visualize"),'">','<span class="fa fa-bar-chart-o"></span>',"</a>",'<ul class="dropdown-menu" role="menu">',"<% _.each( visualizations, function( visualization ){ %>",'<li><a class="visualization-link" href="<%- visualization.href %>"',' target="<%- visualization.target %>">',"<%- visualization.html %>","</a></li>","<% }); %>","</ul>","</div>","<% } %>"],"visualizations");return o.extend({},d.prototype.templates,{warnings:t,visualizations:e})}(),{DatasetListItemEdit:h}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(3),i(1))},function(t,e,i){var n,s;(function(o,a,r){n=[i(12),i(6),i(5)],s=function(t,e,i){"use strict";var n="dataset",s=e.SearchableModelMixin,l=o.Model.extend(e.LoggableMixin).extend(e.mixin(s,{_logNamespace:n,defaults:{state:t.NEW,deleted:!1,purged:!1,name:"(unnamed dataset)",accessible:!0,data_type:"",file_ext:"",file_size:0,meta_files:[],misc_blurb:"",misc_info:"",tags:[]},initialize:function(e,i){this.debug(this+"(Dataset).initialize",e,i),this.get("accessible")||this.set("state",t.NOT_VIEWABLE),this.urls=this._generateUrls(),this._setUpListeners()},_generateUrls:function(){var t=this.get("id");if(!t)return{};var e={purge:"datasets/"+t+"/purge_async",display:"datasets/"+t+"/display/?preview=True",edit:"datasets/"+t+"/edit",download:"datasets/"+t+"/display?to_ext="+this.get("file_ext"),report_error:"dataset/errors?id="+t,rerun:"tool_runner/rerun?id="+t,show_params:"datasets/"+t+"/show_params",visualization:"visualization",meta_download:"dataset/get_metadata_file?hda_id="+t+"&metadata_name="};return a.each(e,function(t,i){e[i]=Galaxy.root+t}),this.urls=e,e},_setUpListeners:function(){this.on("change:state",function(t,e){this.log(this+" has changed state:",t,e),this.inReadyState()&&this.trigger("state:ready",t,e,this.previous("state"))}),this.on("change:id change:file_ext",function(t){this._generateUrls()})},toJSON:function(){var t=o.Model.prototype.toJSON.call(this);return a.extend(t,{urls:this.urls})},isDeletedOrPurged:function(){return this.get("deleted")||this.get("purged")},inReadyState:function(){var e=a.contains(t.READY_STATES,this.get("state"));return this.isDeletedOrPurged()||e},hasDetails:function(){return a.has(this.attributes,"genome_build")},hasData:function(){return this.get("file_size")>0},fetch:function(t){var e=this;return o.Model.prototype.fetch.call(this,t).always(function(){e._generateUrls()})},"delete":function(t){return this.get("deleted")?r.when():this.save({deleted:!0},t)},undelete:function(t){return!this.get("deleted")||this.get("purged")?r.when():this.save({deleted:!1},t)},purge:function(t){if(this.get("purged"))return r.when();t=t||{},t.url=this.urls.purge;var e=this,n=r.ajax(t);return n.done(function(t,i,n){e.set({deleted:!0,purged:!0})}),n.fail(function(n,s,o){var a=i("Unable to purge dataset"),r="Removal of datasets by users is not allowed in this Galaxy instance";n.responseJSON&&n.responseJSON.error?a=n.responseJSON.error:-1!==n.responseText.indexOf(r)&&(a=r),n.responseText=a,e.trigger("error",e,n,t,i(a),{error:a})}),n},searchAttributes:["name","file_ext","genome_build","misc_blurb","misc_info","annotation","tags"],searchAliases:{title:"name",format:"file_ext",database:"genome_build",blurb:"misc_blurb",description:"misc_blurb",info:"misc_info",tag:"tags"},toString:function(){var t=this.get("id")||"";return this.get("name")&&(t='"'+this.get("name")+'",'+t),"Dataset("+t+")"}})),c=o.Collection.extend(e.LoggableMixin).extend({_logNamespace:n,model:l,urlRoot:Galaxy.root+"api/datasets",url:function(){return this.urlRoot},ids:function(){return this.map(function(t){return t.get("id")})},notReady:function(){return this.filter(function(t){return!t.inReadyState()})},haveDetails:function(){return this.all(function(t){return t.hasDetails()})},ajaxQueue:function(t,e){var i=r.Deferred(),n=this.length,s=[];if(!n)return i.resolve([]),i;var o=this.chain().reverse().map(function(a,r){return function(){var l=t.call(a,e);l.done(function(t){i.notify({curr:r,total:n,response:t,model:a})}),l.always(function(t){s.push(t),o.length?o.shift()():i.resolve(s)})}}).value();return o.shift()(),i},matches:function(t){return this.filter(function(e){return e.matches(t)})},toString:function(){return["DatasetAssociationCollection(",this.length,")"].join("")}});return{DatasetAssociation:l,DatasetAssociationCollection:c}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(3),i(1))},function(t,e,i){var n,s;(function(o){n=[i(33),i(6),i(5)],s=function(t,e,i){"use strict";var n=t.DatasetListItemView,s=n.extend({className:n.prototype.className+" history-content",initialize:function(t,e){n.prototype.initialize.call(this,t,e)},toString:function(){var t=this.model?this.model+"":"(no model)";return"HDAListItemView("+t+")"}});return s.prototype.templates=function(){var t=e.wrapTemplate(['<div class="title-bar clear" tabindex="0">','<span class="state-icon"></span>','<div class="title">','<span class="hid"><%- dataset.hid %></span> ','<span class="name"><%- dataset.name %></span>',"</div>","</div>"],"dataset"),s=o.extend({},n.prototype.templates.warnings,{hidden:e.wrapTemplate(["<% if( !dataset.visible ){ %>",'<div class="hidden-msg warningmessagesmall">',i("This dataset has been hidden"),"</div>","<% } %>"],"dataset")});return o.extend({},n.prototype.templates,{titleBar:t,warnings:s})}(),{HDAListItemView:s}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(3))},function(t,e,i){var n,s;(function(o){n=[i(71),i(42),i(6),i(5)],s=function(t,e,i,n){"use strict";var s=t.DatasetAssociation,a=e.HistoryContentMixin,r=s.extend(i.mixin(a,{constructor:function(t,e){a.constructor.call(this,t,e)},defaults:o.extend({},s.prototype.defaults,a.defaults,{model_class:"HistoryDatasetAssociation"}),initialize:function(t,e){s.prototype.initialize.call(this,t,e),a.initialize.call(this,t,e)},toString:function(){var t=this.get("id")||"";return this.get("name")&&(t=this.get("hid")+' :"'+this.get("name")+'",'+t),"HDA("+t+")"}}));return{HistoryDatasetAssociation:r}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(3))},function(t,e,i){var n,s;(function(o){n=[i(12),i(30),i(69),i(6),i(5)],s=function(t,e,i,n,s){"use strict";var a=e.DCListItemView,r=a.extend({className:a.prototype.className+" history-content",_setUpListeners:function(){a.prototype._setUpListeners.call(this),this.listenTo(this.model,{"change:populated change:visible":function(t,e){this.render()}})},_getFoldoutPanelClass:function(){switch(this.model.get("collection_type")){case"list":return i.ListCollectionView;case"paired":return i.PairCollectionView;case"list:paired":return i.ListOfPairsCollectionView}throw new TypeError("Uknown collection_type: "+this.model.get("collection_type"))},_swapNewRender:function(e){a.prototype._swapNewRender.call(this,e);var i=this.model.get("populated")?t.OK:t.RUNNING;return this.$el.addClass("state-"+i),this.$el},toString:function(){var t=this.model?this.model+"":"(no model)";return"HDCAListItemView("+t+")"}});return r.prototype.templates=function(){var t=o.extend({},a.prototype.templates.warnings,{hidden:n.wrapTemplate(["<% if( !collection.visible ){ %>",'<div class="hidden-msg warningmessagesmall">',s("This collection has been hidden"),"</div>","<% } %>"],"collection")}),e=n.wrapTemplate(['<div class="title-bar clear" tabindex="0">','<span class="state-icon"></span>','<div class="title">','<span class="hid"><%- collection.hid %></span> ','<span class="name"><%- collection.name %></span>',"</div>",'<div class="subtitle"></div>',"</div>"],"collection");return o.extend({},a.prototype.templates,{warnings:t,titleBar:e})}(),{HDCAListItemView:r}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(3))},function(t,e,i){var n,s;(function(o,a,r){n=[i(43),i(4),i(6),i(5)],s=function(t,e,i,n){"use strict";var s="history",l=o.Model.extend(i.LoggableMixin).extend(i.mixin(i.SearchableModelMixin,{_logNamespace:s,defaults:{model_class:"History",id:null,name:"Unnamed History",state:"new",deleted:!1},urlRoot:Galaxy.root+"api/histories",initialize:function(e,i,n){n=n||{},this.logger=n.logger||null,this.log(this+".initialize:",e,i,n),this.log("creating history contents:",i),this.contents=new t.HistoryContents(i||[],{historyId:this.get("id")}),this._setUpListeners(),this.updateTimeoutId=null},_setUpListeners:function(){this.on("error",function(t,e,i,n,s){this.errorHandler(t,e,i,n,s)}),this.contents&&this.listenTo(this.contents,"error",function(){this.trigger.apply(this,["error:contents"].concat(a.makeArray(arguments)))}),this.on("change:id",function(t,e){this.contents&&(this.contents.historyId=e)})},errorHandler:function(t,e,i,n,s){this.clearUpdateTimeout()},nice_size:function(){return e.bytesToString(this.get("size"),!0,2)},toJSON:function(){return r.extend(o.Model.prototype.toJSON.call(this),{nice_size:this.nice_size()})},get:function(t){return"nice_size"===t?this.nice_size():o.Model.prototype.get.apply(this,arguments)},ownedByCurrUser:function(){return Galaxy&&Galaxy.user?Galaxy.user.isAnonymous()||Galaxy.user.id!==this.get("user_id")?!1:!0:!1;
},contentsCount:function(){return r.reduce(r.values(this.get("state_details")),function(t,e){return t+e},0)},searchAttributes:["name","annotation","tags"],searchAliases:{title:"name",tag:"tags"},checkForUpdates:function(t){return this.contents.running().length?this.setUpdateTimeout():(this.trigger("ready"),r.isFunction(t)&&t.call(this)),this},setUpdateTimeout:function(t){t=t||l.UPDATE_DELAY;var e=this;return this.clearUpdateTimeout(),this.updateTimeoutId=setTimeout(function(){e.refresh()},t),this.updateTimeoutId},clearUpdateTimeout:function(){this.updateTimeoutId&&(clearTimeout(this.updateTimeoutId),this.updateTimeoutId=null)},refresh:function(t,e){t=t||[],e=e||{};var i=this;e.data=e.data||{},t.length&&(e.data.details=t.join(","));var n=this.contents.fetch(e);return n.done(function(t){i.checkForUpdates(function(){this.fetch()})}),n},_delete:function(t){return this.get("deleted")?a.when():this.save({deleted:!0},t)},purge:function(t){return this.get("purged")?a.when():this.save({deleted:!0,purged:!0},t)},undelete:function(t){return this.get("deleted")?this.save({deleted:!1},t):a.when()},copy:function(t,e,i){if(t=void 0!==t?t:!0,!this.id)throw new Error("You must set the history ID before copying it.");var n={history_id:this.id};t&&(n.current=!0),e&&(n.name=e),i||(n.all_datasets=!1);var s=this,o=a.post(this.urlRoot,n);return t?o.then(function(t){var e=new l(t);return e.setAsCurrent().done(function(){s.trigger("copied",s,t)})}):o.done(function(t){s.trigger("copied",s,t)})},setAsCurrent:function(){var t=this,e=a.getJSON(Galaxy.root+"history/set_as_current?id="+this.id);return e.done(function(){t.trigger("set-as-current",t)}),e},toString:function(){return"History("+this.get("id")+","+this.get("name")+")"}}));l.UPDATE_DELAY=4e3,l.getHistoryData=function(t,e){function i(e){return"current"===t?a.getJSON(Galaxy.root+"history/current_history_json"):a.ajax(Galaxy.root+"api/histories/"+t)}function n(t){return t&&t.empty}function s(t){if(n(t))return[];r.isFunction(o)&&(o=o(t)),r.isFunction(l)&&(l=l(t));var e={};return o.length&&(e.dataset_details=o.join(",")),l.length&&(e.dataset_collection_details=l.join(",")),a.ajax(Galaxy.root+"api/histories/"+t.id+"/contents",{data:e})}e=e||{};var o=e.detailIdsFn||[],l=e.hdcaDetailIds||[],c=a.Deferred(),d=null,h=e.historyFn||i,u=e.contentsFn||s,p=h(t);p.done(function(t){d=t,c.notify({status:"history data retrieved",historyJSON:d})}),p.fail(function(t,e,i){c.reject(t,"loading the history")});var g=p.then(u);return g.then(function(t){c.notify({status:"contents data retrieved",historyJSON:d,contentsJSON:t}),c.resolve(d,t)}),g.fail(function(t,e,i){c.reject(t,"loading the contents",{history:d})}),c};var c={fetch:function(t){return t=t||{},t.data=t.data||this._buildFetchData(t),t.traditional=!0,o.Collection.prototype.fetch.call(this,t)},_fetchOptions:["order","limit","offset","view","keys"],_buildFetchData:function(t){var e={},i=this._fetchDefaults();t=r.defaults(t||{},i),e=r.pick(t,this._fetchOptions);var n=r.has(t,"filters")?t.filters:i.filters||{};return r.isEmpty(n)||r.extend(e,this._buildFetchFilters(n)),e},_fetchDefaults:function(){return{}},_buildFetchFilters:function(t){var e={q:[],qv:[]};return r.each(t,function(t,i){t===!0&&(t="True"),t===!1&&(t="False"),e.q.push(i),e.qv.push(t)}),e}},d=o.Collection.extend(i.LoggableMixin).extend(c).extend({_logNamespace:s,model:l,DEFAULT_ORDER:"update_time",sortOrders:{update_time:{getter:function(t){return new Date(t.get("update_time"))},asc:!1},"update_time-asc":{getter:function(t){return new Date(t.get("update_time"))},asc:!0},name:{getter:function(t){return t.get("name")},asc:!0},"name-dsc":{getter:function(t){return t.get("name")},asc:!1},size:{getter:function(t){return t.get("size")},asc:!1},"size-asc":{getter:function(t){return t.get("size")},asc:!0}},initialize:function(t,e){e=e||{},this.log("HistoryCollection.initialize",arguments),this.includeDeleted=e.includeDeleted||!1,this.setOrder(e.order||this.DEFAULT_ORDER),this.currentHistoryId=e.currentHistoryId,this.allFetched=e.allFetched||!1,this.setUpListeners()},urlRoot:Galaxy.root+"api/histories",url:function(){return this.urlRoot},_fetchDefaults:function(){var t={order:this.order,view:"detailed"};return this.includeDeleted||(t.filters={deleted:!1,purged:!1}),t},setUpListeners:function(){this.on({"change:deleted":function(t){this.debug("change:deleted",this.includeDeleted,t.get("deleted")),!this.includeDeleted&&t.get("deleted")&&this.remove(t)},copied:function(t,e){this.setCurrent(new l(e,[]))},"set-as-current":function(t){var e=this.currentHistoryId;this.trigger("no-longer-current",e),this.currentHistoryId=t.id}})},sort:function(t){return t=t||{},this.setOrder(t.order),o.Collection.prototype.sort.call(this,t)},setOrder:function(t){var e=this,i=this.sortOrders[t];if(!r.isUndefined(i))return e.order=t,e.comparator=function(t,n){var s=e.currentHistoryId;return t.id===s?-1:n.id===s?1:(t=i.getter(t),n=i.getter(n),i.asc?t===n?0:t>n?1:-1:t===n?0:t>n?-1:1)},e.trigger("changed-order",e.order,e),e},fetch:function(t){if(t=t||{},this.allFetched)return a.when({});var e=this,i=r.defaults(t,{remove:!1,offset:e.length>=1?e.length-1:0,order:e.order}),n=t.limit;return r.isUndefined(n)||(i.limit=n),c.fetch.call(this,i).done(function(t){var i=r.isArray(t)?t.length:0;(!n||n>i)&&(e.allFetched=!0,e.trigger("all-fetched",e))})},create:function(t,e,i,n){var s=this,o=a.getJSON(Galaxy.root+"history/create_new_current");return o.done(function(t){s.setCurrent(new l(t,[],i||{}))})},setCurrent:function(t,e){return e=e||{},this.unshift(t,e),this.currentHistoryId=t.get("id"),e.silent||this.trigger("new-current",t,this),this},reset:function(t,e){return this.allFetched=!1,o.Collection.prototype.reset.call(this,t,e)},toString:function(){return"HistoryCollection("+this.length+")"}});return{History:l,HistoryCollection:d}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(1),i(3))},function(t,e,i){var n,s;(function(o,a,r){n=[i(44),i(119),i(6),i(5),i(84)],s=function(t,e,i,n){"use strict";var s="list",l=o.View.extend(i.LoggableMixin).extend({_logNamespace:s,viewClass:t.ListItemView,collectionClass:o.Collection,tagName:"div",className:"list-panel",fxSpeed:"fast",emptyMsg:n("This list is empty"),noneFoundMsg:n("No matching items found"),searchPlaceholder:n("search"),initialize:function(t,i){t=t||{},t.logger&&(this.logger=t.logger),this.log(this+".initialize:",t),this.fxSpeed=a.has(t,"fxSpeed")?t.fxSpeed:this.fxSpeed,this.filters=[],this.searchFor=t.searchFor||"",this.indicator=new e(this.$el),this.selecting=void 0!==t.selecting?t.selecting:!0,this.selected=t.selected||[],this.lastSelected=null,this.dragItems=t.dragItems||!1,this.viewClass=t.viewClass||this.viewClass,this.views=[],this.collection=t.collection||new this.collectionClass([]),this.filters=t.filters||[],this.$scrollContainer=t.$scrollContainer||this.$scrollContainer,this.title=t.title||"",this.subtitle=t.subtitle||"",this._setUpListeners()},freeViews:function(){return a.each(this.views,function(t){t.off()}),this.views=[],this},_setUpListeners:function(){return this.off(),this.on({error:function(t,e,i,n,s){console.error(t,e,i,n,s)},loading:function(){this._showLoadingIndicator("loading...",40)},"loading-done":function(){this._hideLoadingIndicator(40)}}),this.once("rendered",function(){this.trigger("rendered:initial",this)}),this.logger&&this.on("all",function(t){this.log(this+"",arguments)}),this._setUpCollectionListeners(),this._setUpViewListeners(),this},_setUpCollectionListeners:function(){return this.log(this+"._setUpCollectionListeners",this.collection),this.collection.off(),this.listenTo(this.collection,{error:function(t,e,i,n,s){this.trigger("error",t,e,i,n,s)},reset:function(){this.renderItems()},add:this.addItemView,remove:this.removeItemView}),this.logger&&this.listenTo(this.collection,"all",function(t){this.info(this+"(collection)",arguments)}),this},_setUpViewListeners:function(){this.log(this+"._setUpViewListeners"),this.on({"view:selected":function(t,e){if(e&&e.shiftKey&&this.lastSelected){var i=this.viewFromModelId(this.lastSelected);i&&this.selectRange(t,i)}else e&&e.altKey&&!this.selecting&&this.showSelectors();this.selected.push(t.model.id),this.lastSelected=t.model.id},"view:de-selected":function(t,e){this.selected=a.without(this.selected,t.model.id)}})},render:function(t){this.log(this+".render",t);var e=this._buildNewRender();return this._setUpBehaviors(e),this._queueNewRender(e,t),this},_buildNewRender:function(){this.debug(this+"(ListPanel)._buildNewRender");var t=r(this.templates.el({},this));return this._renderControls(t),this._renderTitle(t),this._renderSubtitle(t),this._renderSearch(t),this.renderItems(t),t},_renderControls:function(t){this.debug(this+"(ListPanel)._renderControls");var e=r(this.templates.controls({},this));return t.find(".controls").replaceWith(e),e},_renderTitle:function(t){},_renderSubtitle:function(t){},_queueNewRender:function(t,e){e=void 0===e?this.fxSpeed:e;var i=this;i.log("_queueNewRender:",t,e),r(i).queue("fx",[function(t){this.$el.fadeOut(e,t)},function(e){i._swapNewRender(t),e()},function(t){this.$el.fadeIn(e,t)},function(t){i.trigger("rendered",i),t()}])},_swapNewRender:function(t){return this.$el.empty().attr("class",this.className).append(t.children()),this.selecting&&this.showSelectors(0),this},_setUpBehaviors:function(t){return t=t||this.$el,t.find(".controls [title]").tooltip({placement:"bottom"}),this._renderMultiselectActionMenu(t),this},_renderMultiselectActionMenu:function(t){t=t||this.$el;var e=t.find(".list-action-menu"),i=this.multiselectActions();if(!i.length)return e.empty();var s=r(['<div class="list-action-menu btn-group">','<button class="list-action-menu-btn btn btn-default dropdown-toggle" data-toggle="dropdown">',n("For all selected"),"...","</button>",'<ul class="dropdown-menu pull-right" role="menu">',"</ul>","</div>"].join("")),o=i.map(function(t){var e=['<li><a href="javascript:void(0);">',t.html,"</a></li>"].join("");return r(e).click(function(e){return e.preventDefault(),t.func(e)})});return s.find("ul").append(o),e.replaceWith(s),s},multiselectActions:function(){return[]},$scrollContainer:function(){return this.$el.parent().parent()},$list:function(t){return(t||this.$el).find("> .list-items")},$messages:function(t){return(t||this.$el).find("> .controls .messages")},$emptyMessage:function(t){return(t||this.$el).find("> .empty-message")},renderItems:function(t){t=t||this.$el;var e=this;e.log(this+".renderItems",t);var i=e.$list(t);return e.views=e._filterCollection().map(function(t){return e._createItemView(t).render(0)}),i.empty(),e.views.length?(e._attachItems(t),e.$emptyMessage(t).hide()):e._renderEmptyMessage(t).show(),e.trigger("views:ready",e.views),e.views},_filterCollection:function(){var t=this;return t.collection.filter(a.bind(t._filterItem,t))},_filterItem:function(t){var e=this;return a.every(e.filters.map(function(e){return e.call(t)}))&&(!e.searchFor||t.matchesAll(e.searchFor))},_createItemView:function(t){var e=this._getItemViewClass(t),i=a.extend(this._getItemViewOptions(t),{model:t}),n=new e(i);return this._setUpItemViewListeners(n),n},_getItemViewClass:function(t){return this.viewClass},_getItemViewOptions:function(t){return{fxSpeed:this.fxSpeed,expanded:!1,selectable:this.selecting,selected:a.contains(this.selected,t.id),draggable:this.dragItems}},_setUpItemViewListeners:function(t){var e=this;return this.listenTo(t,"all",function(){var t=Array.prototype.slice.call(arguments,0);t[0]="view:"+t[0],e.trigger.apply(e,t)}),this.listenTo(t,"draggable:dragstart",function(t,e){var i={},n=this.getSelectedModels();i=n.length?n.toJSON():[e.model.toJSON()],t.dataTransfer.setData("text",JSON.stringify(i))},this),e},_attachItems:function(t){return this.$list(t).append(this.views.map(function(t){return t.$el})),this},_renderEmptyMessage:function(t){this.debug("_renderEmptyMessage",t,this.searchFor);var e=this.searchFor?this.noneFoundMsg:this.emptyMsg;return this.$emptyMessage(t).text(e)},expandAll:function(){a.each(this.views,function(t){t.expand()})},collapseAll:function(){a.each(this.views,function(t){t.collapse()})},addItemView:function(t,e,i){this.log(this+".addItemView:",t);var n=this;if(n._filterItem(t)){var s=n._createItemView(t);return r(s).queue("fx",[function(t){n.$emptyMessage().fadeOut(n.fxSpeed,t)},function(t){n._attachView(s),t()}]),s}},_attachView:function(t){var e=this;e.views.push(t),e.$list().append(t.render(0).$el.hide()),e.trigger("view:attached",t),t.$el.slideDown(e.fxSpeed,function(){e.trigger("view:attached:rendered")})},removeItemView:function(t,e,i){this.log(this+".removeItemView:",t);var n=this,s=n.viewFromModel(t);if(s)return n.views=a.without(n.views,s),n.trigger("view:removed",s),r({}).queue("fx",[function(t){s.$el.fadeOut(n.fxSpeed,t)},function(t){s.remove(),n.trigger("view:removed:rendered"),n.views.length?t():n._renderEmptyMessage().fadeIn(n.fxSpeed,t)}]),s},viewFromModelId:function(t){for(var e=0;e<this.views.length;e++)if(this.views[e].model.id===t)return this.views[e]},viewFromModel:function(t){return t?this.viewFromModelId(t.id):void 0},viewsWhereModel:function(t){return this.views.filter(function(e){var i=e.model.toJSON();for(var n in t)if(t.hasOwnProperty(n)&&i[n]!==t[n])return!1;return!0})},viewRange:function(t,e){if(t===e)return t?[t]:[];var i=this.views.indexOf(t),n=this.views.indexOf(e);return-1===i||-1===n?i===n?[]:-1===i?[e]:[t]:n>i?this.views.slice(i,n+1):this.views.slice(n,i+1)},_renderSearch:function(t){return t.find(".controls .search-input").searchInput({placeholder:this.searchPlaceholder,initialVal:this.searchFor,onfirstsearch:a.bind(this._firstSearch,this),onsearch:a.bind(this.searchItems,this),onclear:a.bind(this.clearSearch,this)}),t},_firstSearch:function(t){return this.log("onFirstSearch",t),this.searchItems(t)},searchItems:function(t){return this.searchFor=t,this.trigger("search:searching",t,this),this.renderItems(),this.$("> .controls .search-query").val(t),this},clearSearch:function(t){return this.searchFor="",this.trigger("search:clear",this),this.$("> .controls .search-query").val(""),this.renderItems(),this},THROTTLE_SELECTORS_AT:20,showSelectors:function(t){t=void 0!==t?t:this.fxSpeed,this.selecting=!0,this.$(".list-actions").slideDown(t),t=this.views.length>=this.THROTTLE_SELECTORS_AT?0:t,a.each(this.views,function(e){e.showSelector(t)})},hideSelectors:function(t){t=void 0!==t?t:this.fxSpeed,this.selecting=!1,this.$(".list-actions").slideUp(t),t=this.views.length>=this.THROTTLE_SELECTORS_AT?0:t,a.each(this.views,function(e){e.hideSelector(t)}),this.selected=[],this.lastSelected=null},toggleSelectors:function(){this.selecting?this.hideSelectors():this.showSelectors()},selectAll:function(t){a.each(this.views,function(e){e.select(t)})},deselectAll:function(t){this.lastSelected=null,a.each(this.views,function(e){e.deselect(t)})},selectRange:function(t,e){var i=this.viewRange(t,e);return a.each(i,function(t){t.select()}),i},getSelectedViews:function(){return a.filter(this.views,function(t){return t.selected})},getSelectedModels:function(){return new this.collection.constructor(a.map(this.getSelectedViews(),function(t){return t.model}))},_showLoadingIndicator:function(t,i,n){this.debug("_showLoadingIndicator",this.indicator,t,i,n),i=void 0!==i?i:this.fxSpeed,this.indicator||(this.indicator=new e(this.$el,this.$el.parent()),this.debug(" created",this.indicator)),this.$el.is(":visible")?(this.$el.fadeOut(i),this.indicator.show(t,i,n)):this.indicator.show(0,n)},_hideLoadingIndicator:function(t,e){this.debug("_hideLoadingIndicator",this.indicator,t,e),t=void 0!==t?t:this.fxSpeed,this.indicator&&this.indicator.hide(t,e)},scrollPosition:function(){return this.$scrollContainer().scrollTop()},scrollTo:function(t,e){return e=e||0,this.$scrollContainer().animate({scrollTop:t},e),this},scrollToTop:function(t){return this.scrollTo(0,t)},scrollToItem:function(t,e){if(!t)return this;var i=t.el.offsetTop;return this.scrollTo(i,e)},scrollToId:function(t,e){return this.scrollToItem(this.viewFromModelId(t),e)},events:{"click .select-all":"selectAll","click .deselect-all":"deselectAll"},toString:function(){return"ListPanel("+this.collection+")"}});l.prototype.templates=function(){var t=i.wrapTemplate(["<div>",'<div class="controls"></div>','<div class="list-items"></div>','<div class="empty-message infomessagesmall"></div>',"</div>"]),e=i.wrapTemplate(['<div class="controls">','<div class="title">','<div class="name"><%- view.title %></div>',"</div>",'<div class="subtitle"><%- view.subtitle %></div>','<div class="actions"></div>','<div class="messages"></div>','<div class="search">','<div class="search-input"></div>',"</div>",'<div class="list-actions">','<div class="btn-group">','<button class="select-all btn btn-default"','data-mode="select">',n("All"),"</button>",'<button class="deselect-all btn btn-default"','data-mode="select">',n("None"),"</button>","</div>",'<div class="list-action-menu btn-group">',"</div>","</div>","</div>"]);return{el:t,controls:e}}();var c=l.extend({modelCollectionKey:"contents",initialize:function(t){l.prototype.initialize.call(this,t),this.selecting=void 0!==t.selecting?t.selecting:!1,this.setModel(this.model,t)},setModel:function(t,e){if(e=e||{},this.debug(this+".setModel:",t,e),this.freeModel(),this.freeViews(),t){var i=this.model?this.model.get("id"):null;this.model=t,this.logger&&(this.model.logger=this.logger),this._setUpModelListeners(),this.collection.off(),this.collection=this.model[this.modelCollectionKey]?this.model[this.modelCollectionKey]:e.collection||new this.collectionClass([]),this._setUpCollectionListeners(),i&&t.get("id")!==i&&this.trigger("new-model",this)}return this},freeModel:function(){return this.model&&this.stopListening(this.model),this},_setUpModelListeners:function(){return this.log(this+"._setUpModelListeners",this.model),this.listenTo(this.model,"error",function(){var t=Array.prototype.slice.call(arguments,0);t.unshift("error"),this.trigger.apply(this,t)},this),this},_renderControls:function(t){this.debug(this+"(ListPanel)._renderControls");var e=this.model?this.model.toJSON():{},i=r(this.templates.controls(e,this));return t.find(".controls").replaceWith(i),i},toString:function(){return"ModelListPanel("+this.model+")"}});return c.prototype.templates=function(){var t=i.wrapTemplate(['<div class="controls">','<div class="title">','<div class="name"><%- model.name %></div>',"</div>",'<div class="subtitle"><%- view.subtitle %></div>','<div class="actions"></div>','<div class="messages"></div>','<div class="search">','<div class="search-input"></div>',"</div>",'<div class="list-actions">','<div class="btn-group">','<button class="select-all btn btn-default"','data-mode="select">',n("All"),"</button>",'<button class="deselect-all btn btn-default"','data-mode="select">',n("None"),"</button>","</div>",'<div class="list-action-menu btn-group">',"</div>","</div>","</div>"]);return a.extend(a.clone(l.prototype.templates),{controls:t})}(),{ListPanel:l,ModelListPanel:c}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(3),i(1))},function(t,e,i){var n,s;(function(o,a){n=[i(6),i(5)],s=function(t,e){var i=o.View.extend(t.LoggableMixin).extend(t.HiddenUntilActivatedViewMixin).extend({tagName:"div",className:"tags-display",initialize:function(t){this.listenTo(this.model,"change:tags",function(){this.render()}),this.hiddenUntilActivated(t.$activator,t)},render:function(){var t=this;return this.$el.html(this._template()),this.$input().select2({placeholder:"Add tags",width:"100%",tags:function(){return t._getTagsUsed()}}),this._setUpBehaviors(),this},_template:function(){return['<label class="prompt">',e("Tags"),"</label>",'<input class="tags-input" value="',this.tagsToCSV(),'" />'].join("")},tagsToCSV:function(){var t=this.model.get("tags");return!a.isArray(t)||a.isEmpty(t)?"":t.map(function(t){return a.escape(t)}).sort().join(",")},$input:function(){return this.$el.find("input.tags-input")},_getTagsUsed:function(){return Galaxy.user.get("tags_used")},_setUpBehaviors:function(){var t=this;this.$input().on("change",function(e){t.model.save({tags:e.val},{silent:!0}),e.added&&t._addNewTagToTagsUsed(e.added.text+"")})},_addNewTagToTagsUsed:function(t){var e=Galaxy.user.get("tags_used");a.contains(e,t)||(e.push(t),e.sort(),Galaxy.user.set("tags_used",e))},remove:function(){this.$input.off(),this.stopListening(this.model),o.View.prototype.remove.call(this)},toString:function(){return["TagsEditor(",this.model+"",")"].join("")}});return{TagsEditor:i}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(3))},,function(t,e,i){var n,s;(function(o,a){n=[i(4)],s=function(t){return o.View.extend({initialize:function(e){this.options=t.merge(e,{class_add:"upload-icon-button fa fa-square-o",class_remove:"upload-icon-button fa fa-check-square-o",class_partial:"upload-icon-button fa fa-minus-square-o",collection:null,onchange:function(){},onadd:function(){},onremove:function(){}});var i=this;this.collection=this.options.collection,this.setElement(this._template()),this.rows=[],t.get({url:Galaxy.root+"api/remote_files",success:function(t){i._fill(t)},error:function(){i._fill()}})},_fill:function(e){if(e&&e.length>0){this.$el.find("#upload-ftp-content").html(a(this._templateTable()));var i=0;for(index in e)this.rows.push(this._add(e[index])),i+=e[index].size;if(this.$el.find("#upload-ftp-number").html(e.length+" files"),this.$el.find("#upload-ftp-disk").html(t.bytesToString(i,!0)),this.collection){var n=this;this.$("._has_collection").show(),this.$select_all=a("#upload-selectall"),this.$select_all.addClass(this.options.class_add),this.$select_all.on("click",function(){var t=n.$select_all.hasClass(n.options.class_add);for(index in e){var i=e[index],s=n._find(i);(!s&&t||s&&!t)&&n.rows[index].trigger("click")}}),this._refresh()}}else this.$el.find("#upload-ftp-content").html(a(this._templateInfo()));this.$el.find("#upload-ftp-wait").hide()},_add:function(t){var e=this,i=a(this._templateRow(t)),n=i.find(".icon");if(a(this.el).find("tbody").append(i),this.collection){var s="";s=this._find(t)?this.options.class_remove:this.options.class_add,n.addClass(s),i.on("click",function(){var i=e._find(t);n.removeClass(),i?(e.options.onremove(i),n.addClass(e.options.class_add)):(e.options.onadd(t),n.addClass(e.options.class_remove)),e._refresh()})}else i.on("click",function(){e.options.onchange(t)});return i},_refresh:function(){var t=this.collection.where({file_mode:"ftp",enabled:!0});this.$select_all.removeClass(),0==t.length?this.$select_all.addClass(this.options.class_add):t.length==this.rows.length?this.$select_all.addClass(this.options.class_remove):this.$select_all.addClass(this.options.class_partial)},_find:function(t){var e=this.collection.findWhere({file_path:t.path,file_mode:"ftp",enabled:!0});return e&&e.get("id")},_templateRow:function(e){return'<tr class="upload-ftp-row"><td class="_has_collection" style="display: none;"><div class="icon"/></td><td class="ftp-name">'+e.path+'</td><td class="ftp-size">'+t.bytesToString(e.size)+'</td><td class="ftp-time">'+e.ctime+"</td></tr>"},_templateTable:function(){return'<span style="whitespace: nowrap; float: left;">Available files: </span><span style="whitespace: nowrap; float: right;"><span class="upload-icon fa fa-file-text-o"/><span id="upload-ftp-number"/> <span class="upload-icon fa fa-hdd-o"/><span id="upload-ftp-disk"/></span><table class="grid" style="float: left;"><thead><tr><th class="_has_collection" style="display: none;"><div id="upload-selectall"></th><th>Name</th><th>Size</th><th>Created</th></tr></thead><tbody/></table>'},_templateInfo:function(){return'<div class="upload-ftp-warning warningmessage">Your FTP directory does not contain any files.</div>'},_template:function(){return'<div class="upload-ftp"><div id="upload-ftp-wait" class="upload-ftp-wait fa fa-spinner fa-spin"/><div class="upload-ftp-help">This Galaxy server allows you to upload files via FTP. To upload some files, log in to the FTP server at <strong>'+this.options.ftp_upload_site+'</strong> using your Galaxy credentials (email address and password).</div><div id="upload-ftp-content"/><div>'}})}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(1))},function(t,e,i){var n,s;(function(o,a,r){n=[i(4)],s=function(t){return o.View.extend({options:{class_check:"fa-check-square-o",class_uncheck:"fa-square-o",parameters:[{id:"space_to_tab",title:"Convert spaces to tabs"},{id:"to_posix_lines",title:"Use POSIX standard"}]},initialize:function(t){this.model=t.model,this.setElement(a("<div/>").addClass("upload-settings")),this.$el.append(a("<div/>").addClass("upload-settings-cover")),this.$el.append(a("<table/>").addClass("upload-settings-table ui-table-striped").append("<tbody/>")),this.$cover=this.$(".upload-settings-cover"),this.$table=this.$(".upload-settings-table > tbody"),this.listenTo(this.model,"change",this.render,this),this.model.trigger("change")},render:function(){var t=this;this.$table.empty(),r.each(this.options.parameters,function(e){var i=a("<div/>").addClass("upload-"+e.id+" upload-icon-button fa").addClass(t.model.get(e.id)&&t.options.class_check||t.options.class_uncheck).on("click",function(){t.model.get("enabled")&&t.model.set(e.id,!t.model.get(e.id))});t.$table.append(a("<tr/>").append(a("<td/>").append(i)).append(a("<td/>").append(e.title)))}),this.$cover[this.model.get("enabled")&&"hide"||"show"]()}})}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(1),i(3))},,,function(t,e,i){var n,s,o;(function(i,a){!function(i){s=[],n=i,o="function"==typeof n?n.apply(e,s):n,!(void 0!==o&&(t.exports=o))}(function(){i.fn.extend({hoverhighlight:function(t,e){return t=t||"body",this.size()?(a(this).each(function(){var i=a(this),n=i.data("target");n&&i.mouseover(function(i){a(n,t).css({background:e})}).mouseout(function(t){a(n).css({background:""})})}),this):this}})})}).call(e,i(1),i(1))},function(t,e,i){var n,s,o;(function(i,a){!function(i){s=[],n=i,o="function"==typeof n?n.apply(e,s):n,!(void 0!==o&&(t.exports=o))}(function(){function t(t,n){function s(t){var e=i(this).parent().children("input");e.focus().val("").trigger("clear:searchInput"),n.onclear()}function o(t,e){i(this).trigger("search:searchInput",e),"function"==typeof n.onfirstsearch&&f?(f=!1,n.onfirstsearch(e)):n.onsearch(e)}function r(){return['<input type="text" name="',n.name,'" placeholder="',n.placeholder,'" ','class="search-query ',n.classes,'" ',"/>"].join("")}function l(){return i(r()).focus(function(t){i(this).select()}).keyup(function(t){if(t.preventDefault(),t.stopPropagation(),i(this).val()||i(this).blur(),t.which===u&&n.escWillClear)s.call(this,t);else{var e=i(this).val();t.which===p||n.minSearchLen&&e.length>=n.minSearchLen?o.call(this,t,e):e.length||s.call(this,t)}}).on("change",function(t){o.call(this,t,i(this).val())}).val(n.initialVal)}function c(){return i(['<span class="search-clear fa fa-times-circle" ','title="',e("clear search (esc)"),'"></span>'].join("")).tooltip({placement:"bottom"}).click(function(t){s.call(this,t)})}function d(){return i(['<span class="search-loading fa fa-spinner fa-spin" ','title="',e("loading..."),'"></span>'].join("")).hide().tooltip({placement:"bottom"})}function h(){g.find(".search-loading").toggle(),g.find(".search-clear").toggle()}var u=27,p=13,g=i(t),f=!0,m={initialVal:"",name:"search",placeholder:"search",classes:"",onclear:function(){},onfirstsearch:null,onsearch:function(t){},minSearchLen:0,escWillClear:!0,oninit:function(){}};return"string"===a.type(n)?("toggle-loading"===n&&h(),g):("object"===a.type(n)&&(n=a.extend(!0,{},m,n)),g.addClass("search-input").prepend([l(),c(),d()]))}var e=window._l||function(t){return t};a.fn.extend({searchInput:function(e){return this.each(function(){return t(this,e)})}})})}).call(e,i(1),i(1))},,function(t,e,i){var n,s;n=[],s=function(){function t(t,e){var i=/(-?[0-9\.]+)/g,n=t.toString().toLowerCase()||"",s=e.toString().toLowerCase()||"",o=String.fromCharCode(0),a=n.replace(i,o+"$1"+o).split(o),r=s.replace(i,o+"$1"+o).split(o),l=new Date(n).getTime(),c=l?new Date(s).getTime():null;if(c){if(c>l)return-1;if(l>c)return 1}for(var d,h,u=0,p=Math.max(a.length,r.length);p>u;u++){if(d=parseFloat(a[u])||a[u],h=parseFloat(r[u])||r[u],h>d)return-1;if(d>h)return 1}return 0}return t}.apply(e,n),!(void 0!==s&&(t.exports=s))},function(t,e,i){(function(t,e){!function(i){t.event.props.push("dataTransfer"),i.uploadpost=function(e){var n=i.extend({},{data:{},success:function(){},error:function(){},progress:function(){},url:null,maxfilesize:2048,error_filesize:"File exceeds 2GB. Please use a FTP client.",error_default:"Please make sure the file is available.",error_server:"Upload request failed.",error_login:"Uploads require you to log in."},e),s=n.data;if(s.error_message)return void n.error(s.error_message);var o=new FormData;for(var a in s.payload)o.append(a,s.payload[a]);var r=0;for(var a in s.files){var l=s.files[a];o.append(l.name,l.file,l.file.name),r+=l.file.size}return r>1048576*n.maxfilesize?void n.error(n.error_filesize):(xhr=new XMLHttpRequest,xhr.open("POST",n.url,!0),xhr.setRequestHeader("Accept","application/json"),xhr.setRequestHeader("Cache-Control","no-cache"),xhr.setRequestHeader("X-Requested-With","XMLHttpRequest"),xhr.onreadystatechange=function(){if(xhr.readyState==xhr.DONE){var e=null;if(xhr.responseText)try{e=t.parseJSON(xhr.responseText)}catch(i){e=xhr.responseText}if(xhr.status<200||xhr.status>299){var s=xhr.statusText;403==xhr.status?s=n.error_login:0==xhr.status?s=n.error_server:s||(s=n.error_default),n.error(s+" ("+xhr.status+")")}else n.success(e)}},xhr.upload.addEventListener("progress",function(t){t.lengthComputable&&n.progress(Math.round(100*t.loaded/t.total))},!1),Galaxy.emit.debug("uploadbox::uploadpost()","Posting following data.",n),void xhr.send(o))},i.fn.uploadinput=function(t){var e=this,n=i.extend({},{ondragover:function(){},ondragleave:function(){},onchange:function(){},multiple:!1},t),s=i('<input type="file" style="display: none" '+(n.multiple&&"multiple"||"")+"/>");return e.append(s.change(function(t){n.onchange(t.target.files),i(this).val("")})),e.on("drop",function(t){n.ondragleave(t),t.dataTransfer&&(n.onchange(t.dataTransfer.files),t.preventDefault())}),e.on("dragover",function(t){t.preventDefault(),n.ondragover(t)}),e.on("dragleave",function(t){t.stopPropagation(),n.ondragleave(t)}),{dialog:function(){s.trigger("click")}}},i.fn.uploadbox=function(t){function n(t){if(t&&t.length&&!m){var i=g;return e.each(t,function(t,i){"new"!==t.mode&&e.filter(p,function(e){return e.name===t.name&&e.size===t.size}).length&&(t.duplicate=!0)}),e.each(t,function(t){if(!t.duplicate){var e=String(g++);p[e]=t,u.announce(e,p[e]),f++}}),i}}function s(t){p[t]&&(delete p[t],f--)}function o(){if(0==f||v)return v=!1,m=!1,void u.complete();m=!0;var t=-1;for(var e in p){t=e;break}p[t];s(t),i.uploadpost({url:u.url,data:u.initialize(t),success:function(e){u.success(t,e),o()},error:function(e){u.error(t,e),o()},progress:function(e){u.progress(t,e)}})}function a(){_.dialog()}function r(t){for(t in p)s(t)}function l(){m||(m=!0,o())}function c(){v=!0}function d(t){return u=i.extend({},u,t)}function h(){return window.File&&window.FormData&&window.XMLHttpRequest&&window.FileList}var u=i.extend({},{dragover:function(){},dragleave:function(){},announce:function(t){},initialize:function(t){},progress:function(t,e){},success:function(t,e){},error:function(t,e){alert(e)},complete:function(){}},t),p={},g=0,f=0,m=!1,v=!1,_=i(this).uploadinput({multiple:!0,onchange:function(t){n(t)},ondragover:t.ondragover,ondragleave:t.ondragleave});return{select:a,add:n,remove:s,start:l,stop:c,reset:r,configure:d,compatible:h}}}(t)}).call(e,i(1),i(3))},function(t,e,i){var n=i(10).RightPanel,s=i(7),o=i(109);CurrentHistoryView=i(106).CurrentHistoryView,_l=i(5);var a=n.extend({title:_l("History"),initialize:function(t){n.prototype.initialize.call(this,t);var e=this;this.refreshButton=new s.ButtonLink({id:"history-refresh-button",title:_l("Refresh history"),cls:"panel-header-button",icon:"fa fa-refresh",onclick:function(){e.historyView.loadCurrentHistory();
}}),this.optionsButton=new s.ButtonLink({id:"history-options-button",title:_l("History options"),cls:"panel-header-button",icon:"fa fa-cog"}),this.viewMultiButton=null,t.userIsAnonymous||(this.viewMultiButton=new s.ButtonLink({id:"history-view-multi-button",title:_l("View all histories"),cls:"panel-header-button",icon:"fa fa-columns",href:t.galaxyRoot+"history/view_multiple"})),this.optionsMenu=o(this.optionsButton.$el,{anonymous:t.userIsAnonymous,purgeAllowed:t.allow_user_dataset_purge,root:t.galaxyRoot}),this.historyView=new CurrentHistoryView({purgeAllowed:t.allow_user_dataset_purge,linkTarget:"galaxy_main",$scrollContainer:function(){return this.$el.parent()}})},render:function(){n.prototype.render.call(this),this.$(".unified-panel-header").addClass("history-panel-header"),this.$(".panel-header-buttons").append([this.refreshButton.$el,this.optionsButton.$el,this.viewMultiButton?this.viewMultiButton.$el:null]),this.historyView.setElement(this.$(".history-panel"))},_templateBody:function(t){return['<div class="unified-panel-body unified-panel-body-background">','<div id="current-history-panel" class="history-panel"/>',"</div>"].join("")},toString:function(){return"HistoryPanel"}});t.exports=a},function(t,e,i){(function(e,n){var s=i(10).LeftPanel,o=i(46),a=i(115),r=i(5),l=s.extend({title:r("Tools"),initialize:function(t){s.prototype.initialize.call(this,t),this.log(this+".initialize:",t),this.stored_workflow_menu_entries=t.stored_workflow_menu_entries||[];var e=new o.ToolSearch({search_url:t.search_url,hidden:!1}),i=new o.ToolCollection(t.toolbox);this.tool_panel=new o.ToolPanel({tool_search:e,tools:i,layout:t.toolbox_in_panel}),this.tool_panel_view=new o.ToolPanelView({model:this.tool_panel}),this.uploadButton=new a({nginx_upload_path:t.nginx_upload_path,ftp_upload_site:t.ftp_upload_site,default_genome:t.default_genome,default_extension:t.default_extension})},render:function(){var t=this;s.prototype.render.call(t),t.$(".panel-header-buttons").append(t.uploadButton.$el),t.tool_panel.get("layout").size()>0&&(t.tool_panel_view.render(),t.$(".toolMenu").show()),t.$(".toolMenuContainer").prepend(t.tool_panel_view.$el),t._renderWorkflowMenu(),t.$("a[minsizehint]").click(function(){parent.handle_minwidth_hint&&parent.handle_minwidth_hint(e(t).attr("minsizehint"))})},_renderWorkflowMenu:function(){var t=this;t.$("#internal-workflows").append(t._templateTool({title:r("All workflows"),href:"workflow/list_for_run"})),n.each(t.stored_workflow_menu_entries,function(e){t.$("#internal-workflows").append(t._templateTool({title:e.stored_workflow.name,href:"workflow/run?id="+e.encoded_stored_workflow_id}))})},_templateTool:function(t){return['<div class="toolTitle">','<a href="',Galaxy.root,t.href,'" target="galaxy_main">',t.title,"</a>","</div>"].join("")},_templateBody:function(){return['<div class="unified-panel-body unified-panel-body-background">','<div class="toolMenuContainer">','<div class="toolMenu" style="display: none">','<div id="search-no-results" style="display: none; padding-top: 5px">',"<em><strong>",r("Search did not match any tools."),"</strong></em>","</div>","</div>",'<div class="toolSectionPad"/>','<div class="toolSectionPad"/>','<div class="toolSectionTitle" id="title_XXinternalXXworkflow">',"<span>",r("Workflows"),"</span>","</div>",'<div id="internal-workflows" class="toolSectionBody">','<div class="toolSectionBg"/>',"</div>","</div>","</div>"].join("")},toString:function(){return"ToolPanel"}});t.exports=l}).call(e,i(1),i(3))},,,,,,,,,,function(t,e,i){var n,s;(function(o,a){n=[i(30),i(70),i(6),i(5)],s=function(t,e,i,n){"use strict";var s=t.DCListItemView,r=s.extend({initialize:function(t){s.prototype.initialize.call(this,t)},toString:function(){var t=this.model?this.model+"":"(no model)";return"DCListItemEdit("+t+")"}}),l=t.DCEListItemView,c=l.extend({initialize:function(t){l.prototype.initialize.call(this,t)},toString:function(){var t=this.model?this.model+"":"(no model)";return"DCEListItemEdit("+t+")"}}),d=e.DatasetListItemEdit.extend({initialize:function(t){e.DatasetListItemEdit.prototype.initialize.call(this,t)},_fetchModelDetails:function(){var t=this;return t.model.inReadyState()&&!t.model.hasDetails()?t.model.fetch({silent:!0}):o.when()},_renderDeleteButton:function(){return null},toString:function(){var t=this.model?this.model+"":"(no model)";return"DatasetDCEListItemEdit("+t+")"}});d.prototype.templates=function(){return a.extend({},e.DatasetListItemEdit.prototype.templates,{titleBar:t.DatasetDCEListItemView.prototype.templates.titleBar})}();var h=t.NestedDCDCEListItemView.extend({toString:function(){var t=this.model?this.model+"":"(no model)";return"NestedDCDCEListItemEdit("+t+")"}});return{DCListItemEdit:r,DCEListItemEdit:c,DatasetDCEListItemEdit:d,NestedDCDCEListItemEdit:h}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(1),i(3))},function(t,e,i){var n,s;n=[i(69),i(31),i(99),i(6),i(5),i(16)],s=function(t,e,i,n,s){"use strict";var o=t.CollectionView,a=o.extend({DatasetDCEViewClass:i.DatasetDCEListItemEdit,NestedDCDCEViewClass:i.NestedDCDCEListItemEdit,initialize:function(t){o.prototype.initialize.call(this,t)},_setUpBehaviors:function(t){if(t=t||this.$el,o.prototype._setUpBehaviors.call(this,t),this.model&&Galaxy.user&&!Galaxy.user.isAnonymous()){var e=this,i="> .controls .name";t.find(i).attr("title",s("Click to rename collection")).tooltip({placement:"bottom"}).make_text_editable({on_finish:function(t){var n=e.model.get("name");t&&t!==n?(e.$el.find(i).text(t),e.model.save({name:t}).fail(function(){e.$el.find(i).text(e.model.previous("name"))})):e.$el.find(i).text(n)}})}},toString:function(){return"CollectionViewEdit("+(this.model?this.model.get("name"):"")+")"}}),r=a.extend({DatasetDCEViewClass:i.DatasetDCEListItemEdit,toString:function(){return"ListCollectionViewEdit("+(this.model?this.model.get("name"):"")+")"}}),l=r.extend({toString:function(){return"PairCollectionViewEdit("+(this.model?this.model.get("name"):"")+")"}}),c=l.extend({_setUpBehaviors:function(t){o.prototype._setUpBehaviors.call(this,t)},toString:function(){return"NestedPairCollectionViewEdit("+(this.model?this.model.get("name"):"")+")"}}),d=a.extend({NestedDCDCEViewClass:i.NestedDCDCEListItemEdit.extend({foldoutPanelClass:c}),toString:function(){return"ListOfPairsCollectionViewEdit("+(this.model?this.model.get("name"):"")+")"}});return{CollectionViewEdit:a,ListCollectionViewEdit:r,PairCollectionViewEdit:l,ListOfPairsCollectionViewEdit:d}}.apply(e,n),!(void 0!==s&&(t.exports=s))},function(t,e,i){var n,s;(function(o,a,r,l){n=[i(122),i(86),i(32),i(6),i(5),i(83)],s=function(t,e,i,n,s){"use strict";function c(t){function e(){return i.length||(i=[new RegExp(this.filters[0]),new RegExp(this.filters[1])]),i}t=t||{},t.createPair=t.createPair||function(t){t=t||{};var e=t.listA.splice(t.indexA,1)[0],i=t.listB.splice(t.indexB,1)[0],n=t.listB.indexOf(e),s=t.listA.indexOf(i);return-1!==n&&t.listB.splice(n,1),-1!==s&&t.listA.splice(s,1),this._pair(e,i,{silent:!0})};var i=[];return t.preprocessMatch=t.preprocessMatch||function(t){var i=e.call(this);return a.extend(t,{matchTo:t.matchTo.name.replace(i[0],""),possible:t.possible.name.replace(i[1],"")})},function(e){this.debug("autopair _strategy ---------------------------"),e=e||{};var i,n=e.listA,s=e.listB,o=0,a={score:0,index:null},r=[];for(this.debug("starting list lens:",n.length,s.length),this.debug("bestMatch (starting):",JSON.stringify(a,null," "));o<n.length;){var l=n[o];for(a.score=0,i=0;i<s.length;i++){var c=s[i];if(this.debug(o+":"+l.name),this.debug(i+":"+c.name),n[o]!==s[i]&&(a=t.match.call(this,t.preprocessMatch.call(this,{matchTo:l,possible:c,index:i,bestMatch:a})),this.debug("bestMatch:",JSON.stringify(a,null," ")),1===a.score)){this.debug("breaking early due to perfect match");break}}var d=t.scoreThreshold.call(this);if(this.debug("scoreThreshold:",d),this.debug("bestMatch.score:",a.score),a.score>=d?r.push(t.createPair.call(this,{listA:n,indexA:o,listB:s,indexB:a.index})):o+=1,!n.length||!s.length)return r}return this.debug("paired:",JSON.stringify(r,null," ")),this.debug("autopair _strategy ---------------------------"),r}}function d(t){var e=t.toJSON();return g(e,{historyId:t.historyId})}var h="collections",u=o.View.extend(n.LoggableMixin).extend({_logNamespace:h,tagName:"li",className:"dataset paired",initialize:function(t){this.pair=t.pair||{}},template:a.template(['<span class="forward-dataset-name flex-column"><%- pair.forward.name %></span>','<span class="pair-name-column flex-column">','<span class="pair-name"><%- pair.name %></span>',"</span>",'<span class="reverse-dataset-name flex-column"><%- pair.reverse.name %></span>'].join("")),render:function(){return this.$el.attr("draggable",!0).data("pair",this.pair).html(this.template({pair:this.pair})).addClass("flex-column-container"),this},events:{dragstart:"_dragstart",dragend:"_dragend",dragover:"_sendToParent",drop:"_sendToParent"},_dragstart:function(t){t.currentTarget.style.opacity="0.4",t.originalEvent&&(t=t.originalEvent),t.dataTransfer.effectAllowed="move",t.dataTransfer.setData("text/plain",JSON.stringify(this.pair)),this.$el.parent().trigger("pair.dragstart",[this])},_dragend:function(t){t.currentTarget.style.opacity="1.0",this.$el.parent().trigger("pair.dragend",[this])},_sendToParent:function(t){this.$el.parent().trigger(t)},toString:function(){return"PairView("+this.pair.name+")"}}),p=o.View.extend(n.LoggableMixin).extend({_logNamespace:h,className:"list-of-pairs-collection-creator collection-creator flex-row-container",initialize:function(t){this.metric("PairedCollectionCreator.initialize",t),t=a.defaults(t,{datasets:[],filters:this.DEFAULT_FILTERS,automaticallyPair:!0,strategy:"lcs",matchPercentage:.9,twoPassAutopairing:!0}),this.initialList=t.datasets,this.historyId=t.historyId,this.filters=this.commonFilters[t.filters]||this.commonFilters[this.DEFAULT_FILTERS],a.isArray(t.filters)&&(this.filters=t.filters),this.automaticallyPair=t.automaticallyPair,this.strategy=this.strategies[t.strategy]||this.strategies[this.DEFAULT_STRATEGY],a.isFunction(t.strategy)&&(this.strategy=t.strategy),this.matchPercentage=t.matchPercentage,this.twoPassAutopairing=t.twoPassAutopairing,this.removeExtensions=!0,this.oncancel=t.oncancel,this.oncreate=t.oncreate,this.autoscrollDist=t.autoscrollDist||24,this.unpairedPanelHidden=!1,this.pairedPanelHidden=!1,this.$dragging=null,this.blocking=!1,this._setUpBehaviors(),this._dataSetUp()},commonFilters:{illumina:["_1","_2"],Rs:["_R1","_R2"]},DEFAULT_FILTERS:"illumina",strategies:{simple:"autopairSimple",lcs:"autopairLCS",levenshtein:"autopairLevenshtein"},DEFAULT_STRATEGY:"lcs",_dataSetUp:function(){this.paired=[],this.unpaired=[],this.selectedIds=[],this._sortInitialList(),this._ensureIds(),this.unpaired=this.initialList.slice(0),this.automaticallyPair&&(this.autoPair(),this.once("rendered:initial",function(){this.trigger("autopair")}))},_sortInitialList:function(){this._sortDatasetList(this.initialList)},_sortDatasetList:function(t){return t.sort(function(t,i){return e(t.name,i.name)}),t},_ensureIds:function(){return this.initialList.forEach(function(t){t.hasOwnProperty("id")||(t.id=a.uniqueId())}),this.initialList},_splitByFilters:function(){function t(t,e){return e.test(t.name)}var e=this.filters.map(function(t){return new RegExp(t)}),i=[[],[]];return this.unpaired.forEach(function(n){e.forEach(function(e,s){t(n,e)&&i[s].push(n)})}),i},_addToUnpaired:function(t){var i=function(n,s){if(n===s)return n;var o=Math.floor((s-n)/2)+n,a=e(t.name,this.unpaired[o].name);if(0>a)return i(n,o);if(a>0)return i(o+1,s);for(;this.unpaired[o]&&this.unpaired[o].name===t.name;)o++;return o}.bind(this);this.unpaired.splice(i(0,this.unpaired.length),0,t)},autoPair:function(t){var e=this._splitByFilters(),i=[];return this.twoPassAutopairing&&(i=this.autopairSimple({listA:e[0],listB:e[1]}),e=this._splitByFilters()),t=t||this.strategy,e=this._splitByFilters(),i=i.concat(this[t].call(this,{listA:e[0],listB:e[1]}))},autopairSimple:c({scoreThreshold:function(){return 1},match:function(t){return t=t||{},t.matchTo===t.possible?{index:t.index,score:1}:t.bestMatch}}),autopairLevenshtein:c({scoreThreshold:function(){return this.matchPercentage},match:function(e){e=e||{};var i=t(e.matchTo,e.possible),n=1-i/Math.max(e.matchTo.length,e.possible.length);return n>e.bestMatch.score?{index:e.index,score:n}:e.bestMatch}}),autopairLCS:c({scoreThreshold:function(){return this.matchPercentage},match:function(t){t=t||{};var e=this._naiveStartingAndEndingLCS(t.matchTo,t.possible).length,i=e/Math.max(t.matchTo.length,t.possible.length);return i>t.bestMatch.score?{index:t.index,score:i}:t.bestMatch}}),_naiveStartingAndEndingLCS:function(t,e){for(var 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",'Paired datasets are shown in the <i data-target=".paired-columns">paired section</i>.',"<ul>To pair datasets, you can:","<li>Click a dataset in the ",'<i data-target=".unpaired-columns .forward-column .column-datasets,','.unpaired-columns .forward-column">forward column</i> ',"to select it then click a dataset in the ",'<i data-target=".unpaired-columns .reverse-column .column-datasets,','.unpaired-columns .reverse-column">reverse column</i>.',"</li>",'<li>Click one of the "Pair these datasets" buttons in the ','<i data-target=".unpaired-columns .paired-column .column-datasets,','.unpaired-columns .paired-column">middle column</i> ',"to pair the datasets in a particular row.","</li>",'<li>Click <i data-target=".autopair-link">"Auto-pair"</i> ',"to have your datasets automatically paired based on name.","</li>","</ul>"].join("")),"</p>","<p>",s(["<ul>You can filter what is shown in the unpaired sections by:","<li>Entering partial dataset names in either the ",'<i data-target=".forward-unpaired-filter input">forward filter</i> or ','<i data-target=".reverse-unpaired-filter input">reverse filter</i>.',"</li>","<li>Choosing from a list of preset filters by clicking the ",'<i data-target=".choose-filters-link">"Choose filters" link</i>.',"</li>","<li>Entering regular expressions to match dataset names. See: ",'<a href="https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Regular_Expressions"',' target="_blank">MDN\'s JavaScript Regular Expression Tutorial</a>. ',"Note: forward slashes (\\) are not needed.","</li>","<li>Clearing the filters by clicking the ",'<i data-target=".clear-filters-link">"Clear filters" link</i>.',"</li>","</ul>"].join("")),"</p>","<p>",s(["To unpair individual dataset pairs, click the ",'<i data-target=".unpair-btn">unpair buttons ( <span class="fa fa-unlink"></span> )</i>. 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',"(Note: you do not have to pair all unpaired datasets to finish.)"].join("")),"</p>"].join(""))};var g=function(t,e){var i,n=r.Deferred();if(e=a.defaults(e||{},{datasets:t,oncancel:function(){Galaxy.modal.hide(),n.reject("cancelled")},oncreate:function(t,e){Galaxy.modal.hide(),n.resolve(e)}}),!window.Galaxy||!Galaxy.modal)throw new Error("Galaxy or Galaxy.modal not found");return i=new p(e),Galaxy.modal.show({title:"Create a collection of paired datasets",body:i.$el,width:"80%",height:"800px",closing_events:!0}),i.render(),window.creator=i,n};return{PairedCollectionCreator:p,pairedCollectionCreatorModal:g,createListOfPairsCollection:d}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(3),i(1),i(1))},function(t,e,i){var n,s;(function(o,a,r){n=[i(32),i(41),i(6),i(5)],s=function(t,e,i,n){"use strict";function s(t){var e=t.toJSON(),i=u(e,{creationFn:function(e,i){return e=[{name:"forward",src:"hda",id:e[0].id},{name:"reverse",src:"hda",id:e[1].id}],t.createHDCA(e,"paired",i)}});return i}var l="collections",c=o.View.extend(i.LoggableMixin).extend({_logNamespace:l,tagName:"li",className:"collection-element",initialize:function(t){this.element=t.element||{},this.identifier=t.identifier},render:function(){return this.$el.attr("data-element-id",this.element.id).html(this.template({identifier:this.identifier,element:this.element})),this},template:a.template(['<span class="identifier"><%- identifier %></span>','<span class="name"><%- element.name %></span>'].join("")),destroy:function(){this.off(),this.$el.remove()},toString:function(){return"DatasetCollectionElementView()"}}),d=t.ListCollectionCreator,h=d.extend({elementViewClass:c,collectionClass:e.HistoryPairDatasetCollection,className:"pair-collection-creator collection-creator flex-row-container",_mangleDuplicateNames:function(){},render:function(t,e){return 2===this.workingElements.length?d.prototype.render.call(this,t,e):this._renderInvalid(t,e)},_renderList:function(t,e){var i=this,n=r("<div/>"),s=i.$list();a.each(this.elementViews,function(t){t.destroy(),i.removeElementView(t)}),n.append(i._createForwardElementView().$el),n.append(i._createReverseElementView().$el),s.empty().append(n.children()),a.invoke(i.elementViews,"render")},_createForwardElementView:function(){return this._createElementView(this.workingElements[0],{identifier:"forward"})},_createReverseElementView:function(){return this._createElementView(this.workingElements[1],{identifier:"reverse"})},_createElementView:function(t,e){var i=new this.elementViewClass(a.extend(e,{element:t}));return this.elementViews.push(i),i},swap:function(){this.workingElements=[this.workingElements[1],this.workingElements[0]],this._renderList()},events:a.extend(a.clone(d.prototype.events),{"click .swap":"swap"}),templates:a.extend(a.clone(d.prototype.templates),{middle:a.template(['<div class="collection-elements-controls">','<a class="swap" href="javascript:void(0);" title="',n("Swap forward and reverse datasets"),'">',n("Swap"),"</a>","</div>",'<div class="collection-elements scroll-container flex-row">',"</div>"].join("")),helpContent:a.template(["<p>",n(["Pair collections are permanent collections containing two datasets: one forward and one reverse. 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",n("You may need to "),'<a class="cancel-create" href="javascript:void(0)">',n("cancel"),"</a> ",n("and reselect new elements"),".","</span>","</div>","</div>",'<div class="footer flex-row no-flex">','<div class="actions clear vertically-spaced">','<div class="other-options pull-left">','<button class="cancel-create btn" tabindex="-1">',n("Cancel"),"</button>","</div>","</div>","</div>"].join(""))}),toString:function(){return"PairCollectionCreator"}}),u=function(e,i){return i=i||{},i.title=n("Create a collection from a pair of datasets"),t.collectionCreatorModal(e,i,h)};return{PairCollectionCreator:h,pairCollectionCreatorModal:u,createPairCollection:s}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(3),i(1))},function(t,e,i){var n,s;(function(o,a,r){n=[i(8),i(5)],s=function(t,e){"use strict";var i={defaultName:o.template("Copy of '<%- name %>'"),title:o.template(e("Copying history")+' "<%- name %>"'),submitLabel:e("Copy"),errorMessage:e("History could not be copied"),progressive:e("Copying history"),activeLabel:e("Copy only the active, non-deleted datasets"),allLabel:e("Copy all datasets including deleted ones"),anonWarning:e("As an anonymous user, unless you login or register, you will lose your current history ")+e("after copying this history. "),_template:o.template(["<% if( isAnon ){ %>",'<div class="warningmessage">',"<%- anonWarning %>",e("You can"),' <a href="/user/login">',e("login here"),"</a> ",e("or")," ",' <a href="/user/create">',e("register here"),"</a>.","</div>","<% } %>","<form>",'<label for="copy-modal-title">',e("Enter a title for the new history"),":","</label><br />",'<input id="copy-modal-title" class="form-control" style="width: 100%" value="<%= name %>" />','<p class="invalid-title bg-danger" style="color: red; margin: 8px 0px 8px 0px; display: none">',e("Please enter a valid history title"),"</p>","<% if( allowAll ){ %>","<br />","<p>",e("Choose which datasets from the original history to include:"),"</p>",'<input name="copy-what" type="radio" id="copy-non-deleted" value="copy-non-deleted" ','<% if( copyWhat === "copy-non-deleted" ){ print( "checked" ); } %>/>','<label for="copy-non-deleted"> <%- activeLabel %></label>',"<br />",'<input name="copy-what" type="radio" id="copy-all" value="copy-all" ','<% if( copyWhat === "copy-all" ){ print( "checked" ); } %>/>','<label for="copy-all"> <%- allLabel %></label>',"<% } %>","</form>"].join("")),_showAjaxIndicator:function(){var t='<p><span class="fa fa-spinner fa-spin"></span> '+this.progressive+"...</p>";this.modal.$(".modal-body").empty().append(t).css({"margin-top":"8px"})},dialog:function(t,i,n){function s(){var n=t.$("#copy-modal-title").val();if(!n)return void t.$(".invalid-title").show();var s="copy-all"===t.$('input[name="copy-what"]:checked').val();t.$("button").prop("disabled",!0),l._showAjaxIndicator(),i.copy(!0,n,s).done(function(t){c.resolve(t)}).fail(function(){alert([l.errorMessage,e("Please contact a Galaxy administrator")].join(". 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Click 'Get Data' on the left tool menu to start"),noneFoundMsg:n("No matching datasets found"),HDCAViewClass:l.prototype.HDCAViewClass.extend({foldoutStyle:"drilldown"}),initialize:function(t){t=t||{},this.preferences=new s(o.extend({id:s.storageKey()},o.pick(t,o.keys(s.prototype.defaults)))),l.prototype.initialize.call(this,t),this.panelStack=[],this.currentContentId=t.currentContentId||null},_setUpListeners:function(){l.prototype._setUpListeners.call(this);var t=this;this.on("new-model",function(){t.preferences.set("scrollPosition",0)})},loadCurrentHistory:function(t){this.debug(this+".loadCurrentHistory");var e=this;return this.loadHistoryWithDetails("current",t).then(function(t,i){e.trigger("current-history",e)})},switchToHistory:function(t,e){var i=this,n=function(){return a.getJSON(Galaxy.root+"history/set_as_current?id="+t)};return this.loadHistoryWithDetails(t,e,n).then(function(t,e){i.trigger("switched-history",i)})},createNewHistory:function(t){if(!Galaxy||!Galaxy.user||Galaxy.user.isAnonymous())return this.displayMessage("error",n("You must be logged in to create histories")),r.when();var e=this,i=function(){return a.getJSON(Galaxy.root+"history/create_new_current")};return this.loadHistory(void 0,t,i).then(function(t,i){e.trigger("new-history",e)})},setModel:function(t,e,i){return l.prototype.setModel.call(this,t,e,i),this.model&&(this.log("checking for updates"),this.model.checkForUpdates()),this},_setUpCollectionListeners:function(){l.prototype._setUpCollectionListeners.call(this),this.listenTo(this.collection,"state:ready",function(t,e,i){t.get("visible")||this.storage.get("show_hidden")||this.removeItemView(t)})},_setUpModelListeners:function(){l.prototype._setUpModelListeners.call(this),this.listenTo(this.model,"change:nice_size change:size",function(){this.trigger("history-size-change",this,this.model,arguments)},this)},_setUpBehaviors:function(t){t=t||this.$el;var e=this;return l.prototype._setUpBehaviors.call(e,t),this._debouncedScrollCaptureHandler||(this._debouncedScrollCaptureHandler=o.debounce(function(){e.$el.is(":visible")&&e.preferences.set("scrollPosition",r(this).scrollTop())},40)),e.$scrollContainer().off("scroll",this._debouncedScrollCaptureHandler).on("scroll",this._debouncedScrollCaptureHandler),e},_buildNewRender:function(){if(!this.model)return r();var t=l.prototype._buildNewRender.call(this);return t.find(".search").prependTo(t.find(".controls")),this._renderQuotaMessage(t),t},_renderQuotaMessage:function(t){return t=t||this.$el,r(this.templates.quotaMsg({},this)).prependTo(t.find(".messages"))},_renderEmptyMessage:function(t){var e=this,i=e.$emptyMessage(t),s=r(".toolMenuContainer");return o.isEmpty(e.views)&&!e.searchFor&&Galaxy&&Galaxy.upload&&s.size()?(i.empty(),i.html([n("This history is empty"),". ",n("You can "),'<a class="uploader-link" href="javascript:void(0)">',n("load your own data"),"</a>",n(" or "),'<a class="get-data-link" href="javascript:void(0)">',n("get data from an external source"),"</a>"].join("")),i.find(".uploader-link").click(function(t){Galaxy.upload.show(t)}),i.find(".get-data-link").click(function(t){s.parent().scrollTop(0),s.find('span:contains("Get Data")').click()}),i.show()):l.prototype._renderEmptyMessage.call(this,t)},_renderTags:function(t){var e=this;l.prototype._renderTags.call(e,t),e.preferences.get("tagsEditorShown")&&e.tagsEditor.toggle(!0),e.listenTo(e.tagsEditor,"hiddenUntilActivated:shown hiddenUntilActivated:hidden",function(t){e.preferences.set("tagsEditorShown",t.hidden)})},_renderAnnotation:function(t){var e=this;l.prototype._renderAnnotation.call(e,t),e.preferences.get("annotationEditorShown")&&e.annotationEditor.toggle(!0),e.listenTo(e.annotationEditor,"hiddenUntilActivated:shown hiddenUntilActivated:hidden",function(t){e.preferences.set("annotationEditorShown",t.hidden)})},_swapNewRender:function(t){l.prototype._swapNewRender.call(this,t);var e=this;return o.delay(function(){var t=e.preferences.get("scrollPosition");t&&e.scrollTo(t,0)},10),this},_attachItems:function(t){l.prototype._attachItems.call(this,t);var e=this;return e.currentContentId&&e._setCurrentContentById(e.currentContentId),this},addItemView:function(t,e,i){var n=l.prototype.addItemView.call(this,t,e,i);return n&&this.panelStack.length?this._collapseDrilldownPanel():n},_setUpItemViewListeners:function(t){var e=this;return l.prototype._setUpItemViewListeners.call(e,t),e.listenTo(t,"expanded:drilldown",function(t,e){this._expandDrilldownPanel(e)}),e.listenTo(t,"collapsed:drilldown",function(t,e){this._collapseDrilldownPanel(e)}),this},setCurrentContent:function(t){this.$(".history-content.current-content").removeClass("current-content"),t?(t.$el.addClass("current-content"),this.currentContentId=t.model.id):this.currentContentId=null},_setCurrentContentById:function(t){var e=this.viewFromModelId(t)||null;this.setCurrentContent(e)},_expandDrilldownPanel:function(t){this.panelStack.push(t),this.$("> .controls").add(this.$list()).hide(),t.parentName=this.model.get("name"),this.$el.append(t.render().$el)},_collapseDrilldownPanel:function(t){this.panelStack.pop(),this.render()},listenToGalaxy:function(t){this.listenTo(t,"galaxy_main:load",function(t){var e=t.fullpath,i={display:/datasets\/([a-f0-9]+)\/display/,edit:/datasets\/([a-f0-9]+)\/edit/,report_error:/dataset\/errors\?id=([a-f0-9]+)/,rerun:/tool_runner\/rerun\?id=([a-f0-9]+)/,show_params:/datasets\/([a-f0-9]+)\/show_params/},n=null,s=null;o.find(i,function(t,i){var o=e.match(t);return o&&2==o.length?(n=o[1],s=i,!0):!1}),n="dataset-"+n,this._setCurrentContentById(n)})},connectToQuotaMeter:function(t){return t?(this.listenTo(t,"quota:over",this.showQuotaMessage),this.listenTo(t,"quota:under",this.hideQuotaMessage),this.on("rendered rendered:initial",function(){t&&t.isOverQuota()&&this.showQuotaMessage()}),this):this},clearMessages:function(t){var e=o.isUndefined(t)?this.$messages().children('[class$="message"]'):r(t.currentTarget);return e=e.not(".quota-message"),e.fadeOut(this.fxSpeed,function(){r(this).remove()}),this},showQuotaMessage:function(){var t=this.$(".quota-message");t.is(":hidden")&&t.slideDown(this.fxSpeed)},hideQuotaMessage:function(){var t=this.$(".quota-message");t.is(":hidden")||t.slideUp(this.fxSpeed)},toString:function(){return"CurrentHistoryView("+(this.model?this.model.get("name"):"")+")"}});return c.prototype.templates=function(){var t=i.wrapTemplate(['<div class="quota-message errormessage">',n("You are over your disk quota"),". ",n("Tool execution is on hold until your disk usage drops below your allocated quota"),".","</div>"],"history");return o.extend(o.clone(l.prototype.templates),{quotaMsg:t})}(),{CurrentHistoryView:c}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(3),i(1),i(1))},function(t,e,i){var n,s;(function(o,a,r){n=[i(108),i(43),i(12),i(73),i(104),i(105),i(77),i(68),i(32),i(102),i(101),i(23),i(47),i(5),i(16)],s=function(t,e,i,n,s,l,c,d,h,u,p,g,f,m){"use strict";var v=t.HistoryView,_=v.extend({HDAViewClass:s.HDAListItemEdit,HDCAViewClass:l.HDCAListItemEdit,initialize:function(t){t=t||{},v.prototype.initialize.call(this,t),this.tagsEditor=null,this.annotationEditor=null,this.purgeAllowed=t.purgeAllowed||!1,this.annotationEditorShown=t.annotationEditorShown||!1,this.tagsEditorShown=t.tagsEditorShown||!1},_setUpListeners:function(){var t=this;v.prototype._setUpListeners.call(t),t.on("drop",function(e,i){t.dataDropped(i),t.dropTargetOff()}),t.on("view:attached view:removed",function(){t._renderCounts()})},_setUpCollectionListeners:function(){return v.prototype._setUpCollectionListeners.call(this),this.listenTo(this.collection,{"change:deleted":this._handleHdaDeletionChange,"change:visible":this._handleHdaVisibleChange,"change:purged":function(t){this.model.fetch()}}),this},_setUpModelListeners:function(){return v.prototype._setUpModelListeners.call(this),this.listenTo(this.model,"change:size",this.updateHistoryDiskSize),this},_buildNewRender:function(){var t=v.prototype._buildNewRender.call(this);return this.model?(Galaxy&&Galaxy.user&&Galaxy.user.id&&Galaxy.user.id===this.model.get("user_id")&&(this._renderTags(t),this._renderAnnotation(t)),t):t},renderItems:function(t){var e=v.prototype.renderItems.call(this,t);return this._renderCounts(t),e},_renderCounts:function(t){function e(t,e){return['<a class="',t,'" href="javascript:void(0);">',e,"</a>"].join("")}t=t||this.$el;var i=this.collection.where({deleted:!0}),n=this.collection.where({visible:!1}),s=[];return this.views.length&&s.push([this.views.length,m("shown")].join(" ")),i.length&&s.push(this.showDeleted?e("toggle-deleted-link",m("hide deleted")):[i.length,e("toggle-deleted-link",m("deleted"))].join(" ")),n.length&&s.push(this.showHidden?e("toggle-hidden-link",m("hide hidden")):[n.length,e("toggle-hidden-link",m("hidden"))].join(" ")),t.find("> .controls .subtitle").html(s.join(", "))},_renderTags:function(t){var e=this;this.tagsEditor=new c.TagsEditor({model:this.model,el:t.find(".controls .tags-display"),onshowFirstTime:function(){this.render()},onshow:function(){e.toggleHDATagEditors(!0,e.fxSpeed)},onhide:function(){e.toggleHDATagEditors(!1,e.fxSpeed)},$activator:g({title:m("Edit history tags"),classes:"history-tag-btn",faIcon:"fa-tags"}).appendTo(t.find(".controls .actions"))})},_renderAnnotation:function(t){var e=this;this.annotationEditor=new d.AnnotationEditor({model:this.model,el:t.find(".controls .annotation-display"),onshowFirstTime:function(){this.render()},onshow:function(){e.toggleHDAAnnotationEditors(!0,e.fxSpeed)},onhide:function(){e.toggleHDAAnnotationEditors(!1,e.fxSpeed)},$activator:g({title:m("Edit history annotation"),classes:"history-annotate-btn",faIcon:"fa-comment"}).appendTo(t.find(".controls .actions"))})},_setUpBehaviors:function(t){if(t=t||this.$el,v.prototype._setUpBehaviors.call(this,t),this.model&&Galaxy.user&&!Galaxy.user.isAnonymous()&&Galaxy.user.id===this.model.get("user_id")){var e=this,i="> .controls .name";t.find(i).attr("title",m("Click to rename history")).tooltip({placement:"bottom"}).make_text_editable({on_finish:function(t){var n=e.model.get("name");t&&t!==n?(e.$el.find(i).text(t),e.model.save({name:t}).fail(function(){e.$el.find(i).text(e.model.previous("name"))})):e.$el.find(i).text(n)}})}},multiselectActions:function(){var t=this,e=[{html:m("Hide datasets"),func:function(){var e=n.HistoryDatasetAssociation.prototype.hide;t.getSelectedModels().ajaxQueue(e)}},{html:m("Unhide datasets"),func:function(){var e=n.HistoryDatasetAssociation.prototype.unhide;t.getSelectedModels().ajaxQueue(e)}},{html:m("Delete datasets"),func:function(){var e=n.HistoryDatasetAssociation.prototype["delete"];t.getSelectedModels().ajaxQueue(e)}},{html:m("Undelete datasets"),func:function(){var e=n.HistoryDatasetAssociation.prototype.undelete;t.getSelectedModels().ajaxQueue(e)}}];return t.purgeAllowed&&e.push({html:m("Permanently delete datasets"),func:function(){if(confirm(m("This will permanently remove the data in your datasets. Are you sure?"))){var e=n.HistoryDatasetAssociation.prototype.purge;t.getSelectedModels().ajaxQueue(e)}}}),e=e.concat(t._collectionActions())},_collectionActions:function(){var t=this;return[{html:m("Build Dataset List"),func:function(){h.createListCollection(t.getSelectedModels()).done(function(){t.model.refresh()})}},{html:m("Build Dataset Pair"),func:function(){u.createPairCollection(t.getSelectedModels()).done(function(){t.model.refresh()})}},{html:m("Build List of Dataset Pairs"),func:function(){p.createListOfPairsCollection(t.getSelectedModels()).done(function(){t.model.refresh()})}}]},_attachItems:function(t){return this.$list(t).append(this.views.reverse().map(function(t){return t.$el})),this},_attachView:function(t){var e=this;e.views.unshift(t),e.$list().prepend(t.render(0).$el.hide()),e.trigger("view:attached",t),t.$el.slideDown(e.fxSpeed,function(){e.trigger("view:attached:rendered")})},_getItemViewOptions:function(t){var e=v.prototype._getItemViewOptions.call(this,t);return o.extend(e,{purgeAllowed:this.purgeAllowed,tagsEditorShown:this.tagsEditor&&!this.tagsEditor.hidden,annotationEditorShown:this.annotationEditor&&!this.annotationEditor.hidden}),e},_handleHdaDeletionChange:function(t){t.get("deleted")&&!this.showDeleted&&this.removeItemView(t),this._renderCounts()},_handleHdaVisibleChange:function(t){t.hidden()&&!this.showHidden&&this.removeItemView(t),this._renderCounts()},toggleHDATagEditors:function(t){var e=Array.prototype.slice.call(arguments,1);o.each(this.views,function(t){t.tagsEditor&&t.tagsEditor.toggle.apply(t.tagsEditor,e)})},toggleHDAAnnotationEditors:function(t){var e=Array.prototype.slice.call(arguments,1);o.each(this.views,function(t){t.annotationEditor&&t.annotationEditor.toggle.apply(t.annotationEditor,e)})},events:o.extend(o.clone(v.prototype.events),{"click .show-selectors-btn":"toggleSelectors","click .toggle-deleted-link":function(t){this.toggleShowDeleted()},"click .toggle-hidden-link":function(t){this.toggleShowHidden()}}),updateHistoryDiskSize:function(){this.$el.find(".history-size").text(this.model.get("nice_size"))},dropTargetOn:function(){if(this.dropTarget)return this;this.dropTarget=!0;var t={dragenter:o.bind(this.dragenter,this),dragover:o.bind(this.dragover,this),dragleave:o.bind(this.dragleave,this),drop:o.bind(this.drop,this)},e=this._renderDropTarget();this.$list().before([this._renderDropTargetHelp(),e]);for(var i in t)t.hasOwnProperty(i)&&e.on(i,t[i]);return this},_renderDropTarget:function(){return this.$(".history-drop-target").remove(),a("<div/>").addClass("history-drop-target").css({height:"64px",margin:"0px 10px 10px 10px",border:"1px dashed black","border-radius":"3px"})},_renderDropTargetHelp:function(){return this.$(".history-drop-target-help").remove(),a("<div/>").addClass("history-drop-target-help").css({margin:"10px 10px 4px 10px",color:"grey","font-size":"80%","font-style":"italic"}).text(m("Drag datasets here to copy them to the current history"))},dropTargetOff:function(){if(!this.dropTarget)return this;this.dropTarget=!1;var t=this.$(".history-drop-target").get(0);for(var e in this._dropHandlers)this._dropHandlers.hasOwnProperty(e)&&t.off(e,this._dropHandlers[e]);return this.$(".history-drop-target").remove(),this.$(".history-drop-target-help").remove(),this},dropTargetToggle:function(){return this.dropTarget?this.dropTargetOff():this.dropTargetOn(),this},dragenter:function(t){t.preventDefault(),t.stopPropagation(),this.$(".history-drop-target").css("border","2px solid black")},dragover:function(t){t.preventDefault(),t.stopPropagation()},dragleave:function(t){t.preventDefault(),t.stopPropagation(),this.$(".history-drop-target").css("border","1px dashed black")},drop:function(t){t.preventDefault();var e=t.originalEvent.dataTransfer;e.dropEffect="move";var i=this,n=e.getData("text");try{n=JSON.parse(n)}catch(s){this.warn("error parsing JSON from drop:",n)}return this.trigger("droptarget:drop",t,n,i),!1},dataDropped:function(t){var e=this;return o.isObject(t)&&"HistoryDatasetAssociation"===t.model_class&&t.id?e.model.contents.copy(t.id):r.when();
},toString:function(){return"HistoryViewEdit("+(this.model?this.model.get("name"):"")+")"}});return{HistoryViewEdit:_}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(3),i(1),i(1))},function(t,e,i){var n,s;(function(o,a){n=[i(76),i(75),i(43),i(72),i(74),i(81),i(23),i(47),i(6),i(5),i(84)],s=function(t,e,i,n,s,r,l,c,d,h){"use strict";var u="history",p=d.SessionStorageModel.extend({defaults:{expandedIds:{},show_deleted:!1,show_hidden:!1},addExpanded:function(t){var e="expandedIds";this.save(e,o.extend(this.get(e),o.object([t.id],[t.get("id")])))},removeExpanded:function(t){var e="expandedIds";this.save(e,o.omit(this.get(e),t.id))},toString:function(){return"HistoryPrefs("+this.id+")"}});p.storageKeyPrefix="history:",p.historyStorageKey=function(t){if(!t)throw new Error("HistoryPrefs.historyStorageKey needs valid id: "+t);return p.storageKeyPrefix+t},p.get=function(t){return new p({id:p.historyStorageKey(t)})},p.clearAll=function(t){for(var e in sessionStorage)0===e.indexOf(p.storageKeyPrefix)&&sessionStorage.removeItem(e)};var g=t.ModelListPanel,f=g.extend({_logNamespace:u,HDAViewClass:n.HDAListItemView,HDCAViewClass:s.HDCAListItemView,collectionClass:i.HistoryContents,modelCollectionKey:"contents",tagName:"div",className:g.prototype.className+" history-panel",emptyMsg:h("This history is empty"),noneFoundMsg:h("No matching datasets found"),searchPlaceholder:h("search datasets"),initialize:function(t){g.prototype.initialize.call(this,t),this.linkTarget=t.linkTarget||"_blank"},freeModel:function(){return g.prototype.freeModel.call(this),this.model&&this.model.clearUpdateTimeout(),this},_setUpListeners:function(){g.prototype._setUpListeners.call(this),this.on({error:function(t,e,i,n,s){this.errorHandler(t,e,i,n,s)},"loading-done":function(){this.views.length||this.trigger("empty-history",this)},"views:ready view:attached view:removed":function(t){this._renderSelectButton()}})},loadHistoryWithDetails:function(t,e,i,n){this.info("loadHistoryWithDetails:",t,e,i,n);var s=function(t){return o.values(p.get(t.id).get("expandedIds"))};return this.loadHistory(t,e,i,n,s)},loadHistory:function(t,i,n,s,o){this.info("loadHistory:",t,i,n,s,o);var a=this;i=i||{},a.trigger("loading",a);var r=e.History.getHistoryData(t,{historyFn:n,contentsFn:s,detailIdsFn:i.initiallyExpanded||o});return a._loadHistoryFromXHR(r,i).fail(function(e,n,s){a.trigger("error",a,e,i,h("An error was encountered while "+n),{historyId:t,history:s||{}})}).always(function(){a.trigger("loading-done",a)})},_loadHistoryFromXHR:function(t,e){var i=this;return t.then(function(t,n){i.JSONToModel(t,n,e),i.render()}),t.fail(function(t,e){i.render()}),t},refreshContents:function(t,e){return this.model?this.model.refresh(t,e):a.when()},JSONToModel:function(t,i,n){this.log("JSONToModel:",t,i,n),n=n||{};var s=new e.History(t,i,n);return this.setModel(s),s},setModel:function(t,e){e=e||{},g.prototype.setModel.call(this,t,e),this.model&&this._setUpWebStorage(e.initiallyExpanded,e.show_deleted,e.show_hidden)},_setUpWebStorage:function(t,e,i){return this.storage&&this.stopListening(this.storage),this.storage=new p({id:p.historyStorageKey(this.model.get("id"))}),o.isObject(t)&&this.storage.set("expandedIds",t),o.isBoolean(e)&&this.storage.set("show_deleted",e),o.isBoolean(i)&&this.storage.set("show_hidden",i),this.trigger("new-storage",this.storage,this),this.log(this+" (init'd) storage:",this.storage.get()),this.listenTo(this.storage,{"change:show_deleted":function(t,e){this.showDeleted=e},"change:show_hidden":function(t,e){this.showHidden=e}},this),this.showDeleted=void 0!==e?e:this.storage.get("show_deleted"),this.showHidden=void 0!==i?i:this.storage.get("show_hidden"),this},_buildNewRender:function(){var t=g.prototype._buildNewRender.call(this);return this._renderSelectButton(t),t},_renderSelectButton:function(t){if(t=t||this.$el,!this.multiselectActions().length)return null;if(!this.views.length)return this.hideSelectors(),t.find(".controls .actions .show-selectors-btn").remove(),null;var e=t.find(".controls .actions .show-selectors-btn");return e.size()?e:l({title:h("Operations on multiple datasets"),classes:"show-selectors-btn",faIcon:"fa-check-square-o"}).prependTo(t.find(".controls .actions"))},_getItemViewClass:function(t){var e=t.get("history_content_type");switch(e){case"dataset":return this.HDAViewClass;case"dataset_collection":return this.HDCAViewClass}throw new TypeError("Unknown history_content_type: "+e)},_filterItem:function(t){var e=this;return g.prototype._filterItem.call(e,t)&&(!t.hidden()||e.showHidden)&&(!t.isDeletedOrPurged()||e.showDeleted)},_getItemViewOptions:function(t){var e=g.prototype._getItemViewOptions.call(this,t);return o.extend(e,{linkTarget:this.linkTarget,expanded:!!this.storage.get("expandedIds")[t.id],hasUser:this.model.ownedByCurrUser()})},_setUpItemViewListeners:function(t){var e=this;return g.prototype._setUpItemViewListeners.call(e,t),e.listenTo(t,{expanded:function(t){e.storage.addExpanded(t.model)},collapsed:function(t){e.storage.removeExpanded(t.model)}}),this},getSelectedModels:function(){var t=g.prototype.getSelectedModels.call(this);return t.historyId=this.collection.historyId,t},events:o.extend(o.clone(g.prototype.events),{"click .show-selectors-btn":"toggleSelectors","click .messages [class$=message]":"clearMessages"}),toggleShowDeleted:function(t,e){return t=void 0!==t?t:!this.showDeleted,e=void 0!==e?e:!0,this.showDeleted=t,e&&this.storage.set("show_deleted",t),this.renderItems(),this.trigger("show-deleted",t),this.showDeleted},toggleShowHidden:function(t,e){return t=void 0!==t?t:!this.showHidden,e=void 0!==e?e:!0,this.showHidden=t,e&&this.storage.set("show_hidden",t),this.renderItems(),this.trigger("show-hidden",t),this.showHidden},_firstSearch:function(t){var e=this,i=".history-search-input";return this.log("onFirstSearch",t),e.model.contents.haveDetails()?void e.searchItems(t):(e.$el.find(i).searchInput("toggle-loading"),void e.model.contents.fetchAllDetails({silent:!0}).always(function(){e.$el.find(i).searchInput("toggle-loading")}).done(function(){e.searchItems(e.searchFor)}))},errorHandler:function(t,e,i,n,s){if(this.error(t,e,i,n,s),e&&0===e.status&&0===e.readyState);else if(e&&502===e.status);else{var o=this._parseErrorMessage(t,e,i,n,s);this.$messages().is(":visible")?this.displayMessage("error",o.message,o.details):this.once("rendered",function(){this.displayMessage("error",o.message,o.details)})}},_parseErrorMessage:function(t,e,i,n,s,a){var l=Galaxy.user,c={message:this._bePolite(n),details:{message:n,raven:window.Raven&&o.isFunction(Raven.lastEventId)?Raven.lastEventId():void 0,agent:navigator.userAgent,url:window.Galaxy?Galaxy.lastAjax.url:void 0,data:window.Galaxy?Galaxy.lastAjax.data:void 0,options:e?o.omit(i,"xhr"):i,xhr:e,source:o.isFunction(t.toJSON)?t.toJSON():t+"",user:l instanceof r.User?l.toJSON():l+""}};if(o.extend(c.details,s||{}),e&&o.isFunction(e.getAllResponseHeaders)){var d=e.getAllResponseHeaders();d=o.compact(d.split("\n")),d=o.map(d,function(t){return t.split(": ")}),c.details.xhr.responseHeaders=o.object(d)}return c},_bePolite:function(t){return t=t||h("An error occurred while getting updates from the server"),t+". "+h("Please contact a Galaxy administrator if the problem persists")+"."},displayMessage:function(t,e,i){var n=this;this.scrollToTop();var s=this.$messages(),r=a("<div/>").addClass(t+"message").html(e);if(!o.isEmpty(i)){var l=a('<a href="javascript:void(0)">Details</a>').click(function(){return Galaxy.modal.show(n._messageToModalOptions(t,e,i)),!1});r.append(" ",l)}return s.append(r)},_messageToModalOptions:function(t,e,i){var n=this,s={title:"Details"};if(o.isObject(i)){i=o.omit(i,o.functions(i));var r=JSON.stringify(i,null," "),l=a("<pre/>").text(r);s.body=a("<div/>").append(l)}else s.body=a("<div/>").html(i);return s.buttons={Ok:function(){Galaxy.modal.hide(),n.clearMessages()}},s},clearMessages:function(t){var e=o.isUndefined(t)?this.$messages().children('[class$="message"]'):a(t.currentTarget);return e.fadeOut(this.fxSpeed,function(){a(this).remove()}),this},scrollToHid:function(t){return this.scrollToItem(o.first(this.viewsWhereModel({hid:t})))},toString:function(){return"HistoryView("+(this.model?this.model.get("name"):"")+")"}});return f.prototype.templates=function(){var t=d.wrapTemplate(['<div class="controls">','<div class="title">','<div class="name"><%- history.name %></div>',"</div>",'<div class="subtitle"></div>','<div class="history-size"><%- history.nice_size %></div>','<div class="actions"></div>','<div class="messages">',"<% if( history.deleted && history.purged ){ %>",'<div class="deleted-msg warningmessagesmall">',h("This history has been purged and deleted"),"</div>","<% } else if( history.deleted ){ %>",'<div class="deleted-msg warningmessagesmall">',h("This history has been deleted"),"</div>","<% } else if( history.purged ){ %>",'<div class="deleted-msg warningmessagesmall">',h("This history has been purged"),"</div>","<% } %>","<% if( history.message ){ %>",'<div class="<%= history.message.level || "info" %>messagesmall">',"<%= history.message.text %>","</div>","<% } %>","</div>",'<div class="tags-display"></div>','<div class="annotation-display"></div>','<div class="search">','<div class="search-input"></div>',"</div>",'<div class="list-actions">','<div class="btn-group">','<button class="select-all btn btn-default"','data-mode="select">',h("All"),"</button>",'<button class="deselect-all btn btn-default"','data-mode="select">',h("None"),"</button>","</div>",'<div class="list-action-menu btn-group">',"</div>","</div>","</div>"],"history");return o.extend(o.clone(g.prototype.templates),{controls:t})}(),{HistoryView:f}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(3),i(1))},function(t,e,i){var n,s;(function(o,a){n=[i(47),i(103),i(6),i(5)],s=function(t,e,i,n){"use strict";function s(t,e,i){return a.clone(r).filter(function(n){return t&&!n.anon?!1:!e&&n.purge?!1:(n.href&&(n.href=i+n.href,n.target="galaxy_main"),n.confirm&&(n.func=function(){confirm(n.confirm)&&(galaxy_main.location=n.href)}),!0)})}var r=[{html:n("History Lists"),header:!0},{html:n("Saved Histories"),href:"history/list"},{html:n("Histories Shared with Me"),href:"history/list_shared"},{html:n("History Actions"),header:!0,anon:!0},{html:n("Create New"),func:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.createNewHistory()}},{html:n("Copy History"),func:function(){e(Galaxy.currHistoryPanel.model).done(function(){Galaxy.currHistoryPanel.loadCurrentHistory()})}},{html:n("Share or Publish"),href:"history/sharing"},{html:n("Show Structure"),href:"history/display_structured",anon:!0},{html:n("Extract Workflow"),href:"workflow/build_from_current_history"},{html:n("Delete"),confirm:n("Really delete the current history?"),href:"history/delete_current"},{html:n("Delete Permanently"),confirm:n("Really delete the current history permanently? This cannot be undone."),href:"history/delete_current?purge=True",purge:!0,anon:!0},{html:n("Dataset Actions"),header:!0,anon:!0},{html:n("Copy Datasets"),href:"dataset/copy_datasets"},{html:n("Dataset Security"),href:"root/history_set_default_permissions"},{html:n("Resume Paused Jobs"),href:"history/resume_paused_jobs?current=True",anon:!0},{html:n("Collapse Expanded Datasets"),func:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.collapseAll()}},{html:n("Unhide Hidden Datasets"),anon:!0,func:function(){if(Galaxy&&Galaxy.currHistoryPanel&&confirm(n("Really unhide all hidden datasets?"))){var t=Galaxy.currHistoryPanel.model.contents.hidden();t.ajaxQueue(o.Model.prototype.save,{visible:!0}).done(function(){Galaxy.currHistoryPanel.renderItems()}).fail(function(){alert("There was an error unhiding the datasets"),console.error(arguments)})}}},{html:n("Delete Hidden Datasets"),anon:!0,func:function(){if(Galaxy&&Galaxy.currHistoryPanel&&confirm(n("Really delete all hidden datasets?"))){var t=Galaxy.currHistoryPanel.model.contents.hidden();t.ajaxQueue(o.Model.prototype.save,{deleted:!0,visible:!0}).done(function(){Galaxy.currHistoryPanel.renderItems()}).fail(function(){alert("There was an error deleting the datasets"),console.error(arguments)})}}},{html:n("Purge Deleted Datasets"),confirm:n("Really delete all deleted datasets permanently? This cannot be undone."),href:"history/purge_deleted_datasets",purge:!0,anon:!0},{html:n("Downloads"),header:!0},{html:n("Export Tool Citations"),href:"history/citations",anon:!0},{html:n("Export History to File"),href:"history/export_archive?preview=True",anon:!0},{html:n("Other Actions"),header:!0},{html:n("Import from File"),href:"history/import_archive"}],l=function(e,i){i=i||{};var n=void 0===i.anonymous?!0:i.anonymous,o=i.purgeAllowed||!1,a=s(n,o,Galaxy.root);return new t(e,a)};return l}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(3))},function(t,e,i){var n,s;(function(o,a){n=[i(4),i(80),i(79),i(25),i(7),i(26),i(87)],s=function(t,e,i,n,s,r){return o.View.extend({status_classes:{init:"upload-mode fa fa-exclamation text-primary",ready:"upload-mode fa fa-check text-success",running:"upload-mode fa fa-spinner fa-spin",success:"upload-mode fa fa-check",error:"upload-mode fa fa-exclamation-triangle"},initialize:function(t,e){this.app=t;var i=this;this.model=e.model,this.setElement(this._template(e.model)),this.uploadinput=this.$el.uploadinput({ondragover:function(){i.model.get("enabled")&&i.$el.addClass("warning")},ondragleave:function(){i.$el.removeClass("warning")},onchange:function(t){"running"!=i.model.get("status")&&t&&t.length>0&&(i.model.reset({file_data:t[0],file_name:t[0].name,file_size:t[0].size,file_mode:t[0].mode||"local"}),i._refreshReady())}}),this.button_menu=new s.ButtonMenu({icon:"fa-caret-down",title:"Select",pull:"left"}),this.$("#source").append(this.button_menu.$el),this.button_menu.addMenu({icon:"fa-laptop",title:"Choose local file",onclick:function(){i.uploadinput.dialog()}}),this.app.ftp_upload_site&&this.button_menu.addMenu({icon:"fa-folder-open-o",title:"Choose FTP file",onclick:function(){i._showFtp()}}),this.button_menu.addMenu({icon:"fa-edit",title:"Paste/Fetch data",onclick:function(){i.model.reset({file_mode:"new",file_name:"New File"})}}),this.ftp=new n.View({title:"Choose FTP file:",container:this.$("#source").find(".ui-button-menu"),placement:"right"}),this.settings=new n.View({title:"Upload configuration",container:this.$("#settings"),placement:"bottom"}),this.$("#text-content").on("change input",function(t){i.model.set("url_paste",a(t.target).val()),i.model.set("file_size",a(t.target).val().length),i._refreshReady()}),this.$("#settings").on("click",function(t){i._showSettings()}).on("mousedown",function(t){t.preventDefault()}),this.model.on("change:percentage",function(){i._refreshPercentage()}),this.model.on("change:status",function(){i._refreshStatus()}),this.model.on("change:info",function(){i._refreshInfo()}),this.model.on("change:file_name",function(){i._refreshFileName()}),this.model.on("change:file_mode",function(){i._refreshMode()}),this.model.on("change:file_size",function(){i._refreshFileSize()}),this.model.on("remove",function(){i.remove()}),this.app.collection.on("reset",function(){i.remove()})},render:function(){this.$("#file_name").html(this.model.get("file_name")||"-"),this.$("#file_desc").html(this.model.get("file_desc")||"Unavailable"),this.$("#file_size").html(t.bytesToString(this.model.get("file_size"))),this.$("#status").removeClass().addClass(this.status_classes.init)},remove:function(){o.View.prototype.remove.apply(this)},_refreshReady:function(){this.app.collection.each(function(t){t.set("status",t.get("file_size")>0&&"ready"||"init")})},_refreshMode:function(){var t=this.model.get("file_mode");"new"==t?(this.height=this.$el.height(),this.$("#text").css({width:this.$el.width()-16+"px",top:this.$el.height()-8+"px"}).show(),this.$el.height(this.$el.height()-8+this.$("#text").height()+16),this.$("#text-content").val("").trigger("keyup")):(this.$el.height(this.height),this.$("#text").hide())},_refreshInfo:function(){var t=this.model.get("info");t?this.$("#info-text").html("<strong>Failed: </strong>"+t).show():this.$("#info-text").hide()},_refreshPercentage:function(){var t=parseInt(this.model.get("percentage"));0!=t?this.$(".progress-bar").css({width:t+"%"}):(this.$(".progress-bar").addClass("no-transition"),this.$(".progress-bar").css({width:"0%"}),this.$(".progress-bar")[0].offsetHeight,this.$(".progress-bar").removeClass("no-transition")),100!=t?this.$("#percentage").html(t+"%"):this.$("#percentage").html("Adding to history...")},_refreshStatus:function(){var t=this.model.get("status");this.$("#status").removeClass().addClass(this.status_classes[t]),this.model.set("enabled","running"!=t),this.$("#text-content").attr("disabled",!this.model.get("enabled")),this.$el.removeClass("success danger warning"),("running"==t||"ready"==t)&&this.model.set("percentage",0),"running"==t?this.$("#source").find(".button").addClass("disabled"):this.$("#source").find(".button").removeClass("disabled"),"success"==t&&(this.$el.addClass("success"),this.model.set("percentage",100),this.$("#percentage").html("100%")),"error"==t?(this.$el.addClass("danger"),this.model.set("percentage",0),this.$("#info-progress").hide(),this.$("#info-text").show()):(this.$("#info-progress").show(),this.$("#info-text").hide())},_refreshFileName:function(){this.$("#file_name").html(this.model.get("file_name")||"-")},_refreshFileSize:function(){this.$("#file_size").html(t.bytesToString(this.model.get("file_size")))},_showFtp:function(){if(this.ftp.visible)this.ftp.hide();else{this.ftp.empty();var t=this;this.ftp.append(new i({ftp_upload_site:this.app.ftp_upload_site,onchange:function(e){t.ftp.hide(),"running"!=t.model.get("status")&&e&&(t.model.reset({file_mode:"ftp",file_name:e.path,file_size:e.size,file_path:e.path}),t._refreshReady())}}).$el),this.ftp.show()}},_showSettings:function(){this.settings.visible?this.settings.hide():(this.settings.empty(),this.settings.append(new e(this).$el),this.settings.show())},_template:function(t){return'<tr id="upload-row-'+t.id+'" class="upload-row"><td><div id="source"/><div class="upload-text-column"><div id="text" class="text"><div class="text-info">You can tell Galaxy to download data from web by entering URL in this box (one per line). You can also directly paste the contents of a file.</div><textarea id="text-content" class="text-content form-control"/></div></div></td><td><div id="status"/></td><td><div id="file_desc" class="upload-title"/></td><td><div id="file_name" class="upload-title"/></td><td><div id="file_size" class="upload-size"/></td><td><div id="settings" class="upload-icon-button fa fa-gear"/></td><td><div id="info" class="upload-info"><div id="info-text"/><div id="info-progress" class="progress"><div class="progress-bar progress-bar-success"/><div id="percentage" class="percentage">0%</div></div></div></td></tr>'}})}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(1))},function(t,e,i){var n,s;(function(o,a,r){n=[i(4),i(54),i(110),i(25),i(26),i(7)],s=function(t,e,i,n,s,l){return o.View.extend({select_extension:null,select_genome:null,collection:new e.Collection,initialize:function(t){this.app=t,this.options=t.options,this.list_extensions=t.list_extensions,this.list_genomes=t.list_genomes,this.ftp_upload_site=t.currentFtp();var e=this;this.setElement(this._template()),this.btnStart=new l.Button({title:"Start",onclick:function(){e._eventStart()}}),this.btnClose=new l.Button({title:"Close",onclick:function(){e.app.modal.hide()}});var i=[this.btnStart,this.btnClose];for(var n in i)this.$("#upload-buttons").prepend(i[n].$el);this.select_extension=new s.View({css:"footer-selection",container:this.$("#footer-extension"),data:a.filter(this.list_extensions,function(t){return t.composite_files}),onchange:function(t){e.collection.reset();var i=a.findWhere(e.list_extensions,{id:t});if(i&&i.composite_files)for(var n in i.composite_files){var s=i.composite_files[n];e.collection.add({id:e.collection.size(),file_desc:s.description||s.name})}}}),this.$("#footer-extension-info").on("click",function(t){e._showExtensionInfo({$el:r(t.target),title:e.select_extension.text(),extension:e.select_extension.value(),placement:"top"})}).on("mousedown",function(t){t.preventDefault()}),this.select_genome=new s.View({css:"footer-selection",container:this.$("#footer-genome"),data:this.list_genomes,value:this.options.default_genome}),this.collection.on("add",function(t){e._eventAnnounce(t)}),this.collection.on("change add",function(){e._updateScreen()}).trigger("change"),this.select_extension.options.onchange(this.select_extension.value())},_eventAnnounce:function(t){var e=new i(this,{model:t});this.$("#upload-table > tbody:first").append(e.$el),e.render(),this.collection.length>0?this.$("#upload-table").show():this.$("#upload-table").hide()},_eventStart:function(){var t=this;this.collection.each(function(e){e.set("genome",t.select_genome.value()),e.set("extension",t.select_extension.value())}),r.uploadpost({url:this.app.options.nginx_upload_path,data:this.app.toData(this.collection.filter()),success:function(e){t._eventSuccess(e)},error:function(e){t._eventError(e)},progress:function(e){t._eventProgress(e)}})},_eventProgress:function(t){this.collection.each(function(e){e.set("percentage",t)})},_eventSuccess:function(t){this.collection.each(function(t){t.set("status","success")}),Galaxy.currHistoryPanel.refreshContents()},_eventError:function(t){this.collection.each(function(e){e.set("status","error"),e.set("info",t)})},_showExtensionInfo:function(t){var e=t.$el,i=t.extension,s=t.title,o=a.findWhere(this.list_extensions,{id:i});this.extension_popup&&this.extension_popup.remove(),this.extension_popup=new n.View({placement:t.placement||"bottom",container:e,destroy:!0}),this.extension_popup.title(s),this.extension_popup.empty(),this.extension_popup.append(this._templateDescription(o)),this.extension_popup.show()},_updateScreen:function(){var t=this.collection.first();t&&"running"==t.get("status")?(this.select_genome.disable(),this.select_extension.disable()):(this.select_genome.enable(),this.select_extension.enable()),this.collection.where({status:"ready"}).length==this.collection.length&&this.collection.length>0?(this.btnStart.enable(),this.btnStart.$el.addClass("btn-primary")):(this.btnStart.disable(),this.btnStart.$el.removeClass("btn-primary")),this.collection.length>0?this.$("#upload-table").show():this.$("#upload-table").hide()},_templateDescription:function(t){if(t.description){var e=t.description;return t.description_url&&(e+=' (<a href="'+t.description_url+'" target="_blank">read more</a>)'),e}return"There is no description available for this file extension."},_template:function(){return'<div class="upload-view-composite"><div id="upload-footer" class="upload-footer"><span class="footer-title">Composite Type:</span><span id="footer-extension"/><span id="footer-extension-info" class="upload-icon-button fa fa-search"/> <span class="footer-title">Genome/Build:</span><span id="footer-genome"/></div><div id="upload-box" class="upload-box"><table id="upload-table" class="ui-table-striped" style="display: none;"><thead><tr><th/><th/><th>Description</th><th>Name</th><th>Size</th><th>Settings</th><th>Status</th></tr></thead><tbody></tbody></table></div><div id="upload-buttons" class="upload-buttons"/></div>'}})}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(3),i(1))},function(t,e,i){var n,s;(function(o,a){n=[i(4),i(54),i(80),i(25),i(26)],s=function(t,e,i,n,s){return o.View.extend({status_classes:{init:"upload-icon-button fa fa-trash-o",queued:"upload-icon fa fa-spinner fa-spin",running:"upload-icon fa fa-spinner fa-spin",success:"upload-icon-button fa fa-check",error:"upload-icon-button fa fa-exclamation-triangle"},settings:null,select_genome:null,select_extension:null,initialize:function(t,e){this.app=t;var i=this;this.model=e.model,this.setElement(this._template(e.model)),this.settings=new n.View({title:"Upload configuration",container:this.$("#settings"),placement:"bottom"});var o=this.app.select_genome.value();this.select_genome=new s.View({css:"upload-genome",onchange:function(t){i.model.set("genome",t)},data:i.app.list_genomes,container:this.$("#genome"),value:o}),this.model.set("genome",o);var r=this.app.select_extension.value();this.select_extension=new s.View({css:"upload-extension",onchange:function(t){i.model.set("extension",t)},data:i.app.list_extensions,container:this.$("#extension"),value:r}),this.model.set("extension",r),this.$("#symbol").on("click",function(){i._removeRow()}),this.$("#extension-info").on("click",function(t){i.app.showExtensionInfo({$el:a(t.target),title:i.select_extension.text(),extension:i.select_extension.value()})}).on("mousedown",function(t){t.preventDefault()}),this.$("#settings").on("click",function(t){i._showSettings()}).on("mousedown",function(t){t.preventDefault()}),this.$("#text-content").on("change input",function(t){i.model.set("url_paste",a(t.target).val()),i.model.set("file_size",a(t.target).val().length)}),this.model.on("change:percentage",function(){i._refreshPercentage()}),this.model.on("change:status",function(){i._refreshStatus()}),this.model.on("change:info",function(){i._refreshInfo()}),this.model.on("change:genome",function(){i._refreshGenome()}),this.model.on("change:extension",function(){i._refreshExtension()}),this.model.on("change:file_size",function(){i._refreshFileSize()}),this.model.on("remove",function(){i.remove()}),this.app.collection.on("reset",function(){i.remove()})},render:function(){var e=this.model.get("file_name"),i=this.model.get("file_size"),n=this.model.get("file_mode");this.$("#title").html(e),this.$("#size").html(t.bytesToString(i)),this.$("#mode").removeClass().addClass("upload-mode").addClass("text-primary"),"new"==n&&(this.$("#text").css({width:this.$el.width()-16+"px",top:this.$el.height()-8+"px"}).show(),this.$el.height(this.$el.height()-8+this.$("#text").height()+16),this.$("#mode").addClass("fa fa-edit")),"local"==n&&this.$("#mode").addClass("fa fa-laptop"),"ftp"==n&&this.$("#mode").addClass("fa fa-folder-open-o")},remove:function(){this.select_genome.remove(),this.select_extension.remove(),o.View.prototype.remove.apply(this)},_refreshExtension:function(){this.select_extension.value(this.model.get("extension"))},_refreshGenome:function(){this.select_genome.value(this.model.get("genome"))},_refreshInfo:function(){var t=this.model.get("info");t?this.$("#info").html("<strong>Failed: </strong>"+t).show():this.$("#info").hide()},_refreshPercentage:function(){var t=parseInt(this.model.get("percentage"));this.$(".progress-bar").css({width:t+"%"}),100!=t?this.$("#percentage").html(t+"%"):this.$("#percentage").html("Adding to history...")},_refreshStatus:function(){var t=this.model.get("status");this.$("#symbol").removeClass().addClass(this.status_classes[t]),this.model.set("enabled","init"==t);var e=this.model.get("enabled");this.$("#text-content").attr("disabled",!e),e?(this.select_genome.enable(),this.select_extension.enable()):(this.select_genome.disable(),this.select_extension.disable()),"success"==t&&(this.$el.addClass("success"),this.$("#percentage").html("100%")),"error"==t&&(this.$el.addClass("danger"),this.$(".progress").remove())},_refreshFileSize:function(){var e=this.model.get("file_size");this.$("#size").html(t.bytesToString(e))},_removeRow:function(){var t=this.model.get("status");("init"==t||"success"==t||"error"==t)&&this.app.collection.remove(this.model)},_showSettings:function(){this.settings.visible?this.settings.hide():(this.settings.empty(),this.settings.append(new i(this).$el),this.settings.show())},_template:function(t){return'<tr id="upload-row-'+t.id+'" class="upload-row"><td><div class="upload-text-column"><div id="mode"/><div id="title" class="upload-title"/><div id="text" class="text"><div class="text-info">You can tell Galaxy to download data from web by entering URL in this box (one per line). You can also directly paste the contents of a file.</div><textarea id="text-content" class="text-content form-control"/></div></div></td><td><div id="size" class="upload-size"/></td><td><div id="extension" class="upload-extension" style="float: left;"/>  <div id="extension-info" class="upload-icon-button fa fa-search"/></td><td><div id="genome" class="upload-genome"/></td><td><div id="settings" class="upload-settings upload-icon-button fa fa-gear"/></td><td><div id="info" class="upload-info"><div class="progress"><div class="progress-bar progress-bar-success"/><div id="percentage" class="percentage">0%</div></div></div></td><td><div id="symbol" class="'+this.status_classes.init+'"/></td></tr>'}})}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(1))},function(t,e,i){var n,s;(function(o,a,r){n=[i(4),i(54),i(112),i(79),i(25),i(26),i(7),i(87)],s=function(t,e,i,n,s,l,c){return o.View.extend({select_extension:null,select_genome:null,uploadbox:null,upload_size:0,collection:new e.Collection,ftp:null,counter:{announce:0,success:0,error:0,running:0,reset:function(){this.announce=this.success=this.error=this.running=0}},initialize:function(t){this.app=t,this.options=t.options,this.list_extensions=t.list_extensions,this.list_genomes=t.list_genomes,this.ui_button=t.ui_button,this.ftp_upload_site=t.currentFtp();var e=this;this.setElement(this._template()),this.btnLocal=new c.Button({id:"btn-local",title:"Choose local file",onclick:function(){e.uploadbox.select()},icon:"fa fa-laptop"}),this.btnFtp=new c.Button({id:"btn-ftp",title:"Choose FTP file",onclick:function(){e._eventFtp()},icon:"fa fa-folder-open-o"}),this.btnCreate=new c.Button({id:"btn-new",title:"Paste/Fetch data",onclick:function(){e._eventCreate()},icon:"fa fa-edit"}),this.btnStart=new c.Button({id:"btn-start",title:"Start",onclick:function(){e._eventStart()}}),this.btnStop=new c.Button({id:"btn-stop",title:"Pause",onclick:function(){e._eventStop()}}),this.btnReset=new c.Button({id:"btn-reset",title:"Reset",onclick:function(){e._eventReset()}}),this.btnClose=new c.Button({id:"btn-close",title:"Close",onclick:function(){e.app.modal.hide()}});var i=[this.btnLocal,this.btnFtp,this.btnCreate,this.btnStop,this.btnReset,this.btnStart,this.btnClose];for(var n in i)this.$("#upload-buttons").prepend(i[n].$el);var e=this;this.uploadbox=this.$("#upload-box").uploadbox({url:this.app.options.nginx_upload_path,announce:function(t,i){e._eventAnnounce(t,i)},initialize:function(t){return e.app.toData([e.collection.get(t)],e.history_id)},progress:function(t,i){e._eventProgress(t,i)},success:function(t,i){e._eventSuccess(t,i)},error:function(t,i){e._eventError(t,i)},complete:function(){e._eventComplete()},ondragover:function(){e.$(".upload-box").addClass("highlight")},ondragleave:function(){e.$(".upload-box").removeClass("highlight")}}),this.ftp=new s.View({title:"FTP files",container:this.btnFtp.$el}),this.select_extension=new l.View({css:"footer-selection",container:this.$("#footer-extension"),data:a.filter(this.list_extensions,function(t){return!t.composite_files}),value:this.options.default_extension,onchange:function(t){e.updateExtension(t)}}),e.$("#footer-extension-info").on("click",function(t){e.showExtensionInfo({$el:r(t.target),title:e.select_extension.text(),extension:e.select_extension.value(),placement:"top"})}).on("mousedown",function(t){t.preventDefault()}),this.select_genome=new l.View({css:"footer-selection",container:this.$("#footer-genome"),data:this.list_genomes,value:this.options.default_genome,onchange:function(t){e.updateGenome(t)}}),this.collection.on("remove",function(t){e._eventRemove(t)}),this._updateScreen()},_eventAnnounce:function(t,n){this.counter.announce++;var s=new e.Model({id:t,file_name:n.name,file_size:n.size,file_mode:n.mode||"local",file_path:n.path,file_data:n});this.collection.add(s);var o=new i(this,{model:s});this.$("#upload-table > tbody:first").append(o.$el),this._updateScreen(),o.render()},_eventProgress:function(t,e){var i=this.collection.get(t);i.set("percentage",e),this.ui_button.set("percentage",this._uploadPercentage(e,i.get("file_size")));
},_eventSuccess:function(t,e){var i=this.collection.get(t);i.set("percentage",100),i.set("status","success"),this.ui_button.set("percentage",this._uploadPercentage(100,i.get("file_size"))),this.upload_completed+=100*i.get("file_size"),this.counter.announce--,this.counter.success++,this._updateScreen(),Galaxy.currHistoryPanel.refreshContents()},_eventError:function(t,e){var i=this.collection.get(t);i.set("percentage",100),i.set("status","error"),i.set("info",e),this.ui_button.set("percentage",this._uploadPercentage(100,i.get("file_size"))),this.ui_button.set("status","danger"),this.upload_completed+=100*i.get("file_size"),this.counter.announce--,this.counter.error++,this._updateScreen()},_eventComplete:function(){this.collection.each(function(t){"queued"==t.get("status")&&t.set("status","init")}),this.counter.running=0,this._updateScreen()},_eventRemove:function(t){var e=t.get("status");"success"==e?this.counter.success--:"error"==e?this.counter.error--:this.counter.announce--,this.uploadbox.remove(t.id),this._updateScreen()},showExtensionInfo:function(t){var e=this,i=t.$el,n=t.extension,o=t.title,r=a.findWhere(e.list_extensions,{id:n});this.extension_popup&&this.extension_popup.remove(),this.extension_popup=new s.View({placement:t.placement||"bottom",container:i}),this.extension_popup.title(o),this.extension_popup.empty(),this.extension_popup.append(this._templateDescription(r)),this.extension_popup.show()},_eventFtp:function(){if(this.ftp.visible)this.ftp.hide();else{this.ftp.empty();var t=this;this.ftp.append(new n({collection:this.collection,ftp_upload_site:this.ftp_upload_site,onadd:function(e){t.uploadbox.add([{mode:"ftp",name:e.path,size:e.size,path:e.path}])},onremove:function(e){t.collection.remove(e)}}).$el),this.ftp.show()}},_eventCreate:function(){this.uploadbox.add([{name:"New File",size:0,mode:"new"}])},_eventStart:function(){if(!(0==this.counter.announce||this.counter.running>0)){var t=this;this.upload_size=0,this.upload_completed=0,this.collection.each(function(e){"init"==e.get("status")&&(e.set("status","queued"),t.upload_size+=e.get("file_size"))}),this.ui_button.set("percentage",0),this.ui_button.set("status","success"),this.counter.running=this.counter.announce,this.history_id=this.app.currentHistory(),this.uploadbox.start(),this._updateScreen()}},_eventStop:function(){this.counter.running>0&&(this.ui_button.set("status","info"),r("#upload-info").html("Queue will pause after completing the current file..."),this.uploadbox.stop())},_eventReset:function(){0==this.counter.running&&(this.collection.reset(),this.counter.reset(),this.uploadbox.reset(),this.select_extension.value(this.options.default_extension),this.select_genome.value(this.options.default_genome),this.ui_button.set("percentage",0),this._updateScreen())},updateExtension:function(t,e){var i=this;this.collection.each(function(n){"init"!=n.get("status")||n.get("extension")!=i.options.default_extension&&e||n.set("extension",t)})},updateGenome:function(t,e){var i=this;this.collection.each(function(n){"init"!=n.get("status")||n.get("genome")!=i.options.default_genome&&e||n.set("genome",t)})},_updateScreen:function(){0==this.counter.announce?this.uploadbox.compatible()?message=" ":message="Browser does not support Drag & Drop. Try Firefox 4+, Chrome 7+, IE 10+, Opera 12+ or Safari 6+.":0==this.counter.running?message="You added "+this.counter.announce+" file(s) to the queue. Add more files or click 'Start' to proceed.":message="Please wait..."+this.counter.announce+" out of "+this.counter.running+" remaining.",this.$("#upload-info").html(message),0==this.counter.running&&this.counter.announce+this.counter.success+this.counter.error>0?this.btnReset.enable():this.btnReset.disable(),0==this.counter.running&&this.counter.announce>0?(this.btnStart.enable(),this.btnStart.$el.addClass("btn-primary")):(this.btnStart.disable(),this.btnStart.$el.removeClass("btn-primary")),this.counter.running>0?this.btnStop.enable():this.btnStop.disable(),0==this.counter.running?(this.btnLocal.enable(),this.btnFtp.enable(),this.btnCreate.enable()):(this.btnLocal.disable(),this.btnFtp.disable(),this.btnCreate.disable()),this.ftp_upload_site?this.btnFtp.$el.show():this.btnFtp.$el.hide(),this.counter.announce+this.counter.success+this.counter.error>0?(this.$("#upload-table").show(),this.$(".upload-helper").hide()):(this.$("#upload-table").hide(),this.$(".upload-helper").show())},_uploadPercentage:function(t,e){return(this.upload_completed+t*e)/this.upload_size},_templateDescription:function(t){if(t.description){var e=t.description;return t.description_url&&(e+=' (<a href="'+t.description_url+'" target="_blank">read more</a>)'),e}return"There is no description available for this file extension."},_template:function(){return'<div class="upload-view-default"><div class="upload-top"><h6 id="upload-info" class="upload-info"/></div><div id="upload-box" class="upload-box"><div class="upload-helper"><i class="fa fa-files-o"/>Drop files here</div><table id="upload-table" class="ui-table-striped" style="display: none;"><thead><tr><th>Name</th><th>Size</th><th>Type</th><th>Genome</th><th>Settings</th><th>Status</th><th/></tr></thead><tbody/></table></div><div id="upload-footer" class="upload-footer"><span class="footer-title">Type (set all):</span><span id="footer-extension"/><span id="footer-extension-info" class="upload-icon-button fa fa-search"/> <span class="footer-title">Genome (set all):</span><span id="footer-genome"/></div><div id="upload-buttons" class="upload-buttons"/></div>'}})}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(3),i(1))},function(t,e,i){var n,s;(function(i,o){n=[],s=function(){var t=i.Model.extend({defaults:{icon:"fa-upload",tooltip:"Download from URL or upload files from disk",label:"Load Data",percentage:0,status:""}}),e=i.View.extend({model:null,initialize:function(t){var e=this,i=t.model;this.setElement(this._template()),this.$el.on("click",function(e){t.onclick(e)}),this.$el.tooltip({title:i.get("tooltip"),placement:"bottom"}),i.on("change:percentage",function(){e._percentage(i.get("percentage"))}),i.on("change:status",function(){e._status(i.get("status"))});var e=this;o(window).on("beforeunload",function(){var e="";return t.onunload&&(e=t.onunload()),""!=e?e:void 0})},_status:function(t){var e=this.$el.find(".progress-bar");e.removeClass(),e.addClass("progress-bar"),e.addClass("progress-bar-notransition"),""!=t&&e.addClass("progress-bar-"+t)},_percentage:function(t){var e=this.$el.find(".progress-bar");e.css({width:t+"%"})},_template:function(){return'<div class="upload-button"><div class="progress"><div class="progress-bar"/><a class="panel-header-button" href="javascript:void(0)" id="tool-panel-upload-button"><span class="fa fa-upload"/></a></div></div>'}});return{Model:t,View:e}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(1))},function(t,e,i){var n,s;(function(o){n=[i(4),i(8),i(27),i(114),i(113),i(111)],s=function(t,e,i,n,s,a){return o.View.extend({options:{nginx_upload_path:"",ftp_upload_site:"n/a",default_genome:"?",default_extension:"auto",height:500,width:900,auto:{id:"auto",text:"Auto-detect",description:"This system will try to detect the file type automatically. If your file is not detected properly as one of the known formats, it most likely means that it has some format problems (e.g., different number of columns on different rows). You can still coerce the system to set your data to the format you think it should be. You can also upload compressed files, which will automatically be decompressed."}},modal:null,ui_button:null,current_history:null,list_extensions:[],list_genomes:[],initialize:function(e){var i=this;this.options=t.merge(e,this.options),this.ui_button=new n.Model,this.ui_button_view=new n.View({model:this.ui_button,onclick:function(t){t.preventDefault(),i.show()},onunload:function(){var t=i.ui_button.get("percentage",0);return t>0&&100>t?"Several uploads are queued.":void 0}}),this.setElement(this.ui_button_view.$el);var i=this;t.get({url:Galaxy.root+"api/datatypes?extension_only=False",success:function(t){for(key in t)i.list_extensions.push({id:t[key].extension,text:t[key].extension,description:t[key].description,description_url:t[key].description_url,composite_files:t[key].composite_files});i.list_extensions.sort(function(t,e){var i=t.text&&t.text.toLowerCase(),n=e.text&&e.text.toLowerCase();return i>n?1:n>i?-1:0}),i.options.datatypes_disable_auto||i.list_extensions.unshift(i.options.auto)}}),t.get({url:Galaxy.root+"api/genomes",success:function(t){for(key in t)i.list_genomes.push({id:t[key][1],text:t[key][0]});i.list_genomes.sort(function(t,e){return t.id==i.options.default_genome?-1:e.id==i.options.default_genome?1:t.text>e.text?1:t.text<e.text?-1:0})}})},show:function(){var t=this;return Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.model?(this.current_user=Galaxy.user.id,this.modal||(this.tabs=new i.View,this.default_view=new s(this),this.tabs.add({id:"regular",title:"Regular",$el:this.default_view.$el}),this.composite_view=new a(this),this.tabs.add({id:"composite",title:"Composite",$el:this.composite_view.$el}),this.modal=new e.View({title:"Download from web or upload from disk",body:this.tabs.$el,height:this.options.height,width:this.options.width,closing_events:!0,title_separator:!1})),void this.modal.show()):void window.setTimeout(function(){t.show()},500)},currentHistory:function(){return this.current_user&&Galaxy.currHistoryPanel.model.get("id")},currentFtp:function(){return this.current_user&&this.options.ftp_upload_site},toData:function(t,e){var i={payload:{tool_id:"upload1",history_id:e||this.currentHistory(),inputs:{}},files:[],error_message:null};if(t&&t.length>0){var n={};n.dbkey=t[0].get("genome",null),n.file_type=t[0].get("extension",null);for(var s in t){var o=t[s];if(o.set("status","running"),!(o.get("file_size")>0)){i.error_message="Upload content incomplete.",o.set("status","error"),o.set("info",i.error_message);break}var a="files_"+s+"|";switch(n[a+"type"]="upload_dataset",n[a+"space_to_tab"]=o.get("space_to_tab")&&"Yes"||null,n[a+"to_posix_lines"]=o.get("to_posix_lines")&&"Yes"||null,o.get("file_mode")){case"new":n[a+"url_paste"]=o.get("url_paste");break;case"ftp":n[a+"ftp_files"]=o.get("file_path");break;case"local":i.files.push({name:a+"file_data",file:o.get("file_data")})}}i.payload.inputs=JSON.stringify(n)}return i}})}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2))},,,,function(t,e,i){var n,s,o;(function(i,a){!function(i,a){s=[],n=a,o="function"==typeof n?n.apply(e,s):n,!(void 0!==o&&(t.exports=o))}(this,function(){function t(t,e){function n(){var i=['<div class="loading-indicator">','<div class="loading-indicator-text">','<span class="fa fa-spinner fa-spin fa-lg"></span>','<span class="loading-indicator-message">loading...</span>',"</div>","</div>"].join("\n"),n=a(i).hide().css(e.css||{position:"fixed"}),s=n.children(".loading-indicator-text");return e.cover?(n.css({"z-index":2,top:t.css("top"),bottom:t.css("bottom"),left:t.css("left"),right:t.css("right"),opacity:.5,"background-color":"white","text-align":"center"}),s=n.children(".loading-indicator-text").css({"margin-top":"20px"})):(s=n.children(".loading-indicator-text").css({margin:"12px 0px 0px 10px",opacity:"0.85",color:"grey"}),s.children(".loading-indicator-message").css({margin:"0px 8px 0px 0px","font-style":"italic"})),n}var s=this;return e=i.extend({cover:!1},e||{}),s.show=function(e,i,o){return e=e||"loading...",i=i||"fast",t.parent().find(".loading-indicator").remove(),s.$indicator=n().insertBefore(t),s.message(e),s.$indicator.fadeIn(i,o),s},s.message=function(t){s.$indicator.find("i").text(t)},s.hide=function(t,e){return t=t||"fast",s.$indicator&&s.$indicator.size()?s.$indicator.fadeOut(t,function(){s.$indicator.remove(),e&&e()}):e&&e(),s},s}return t})}).call(e,i(1),i(1))},,,function(t,e,i){var n,s;n=[],s=function(){function t(t,e){if(0===t.length)return e.length;if(0===e.length)return t.length;var i,n=[];for(i=0;i<=e.length;i++)n[i]=[i];var s;for(s=0;s<=t.length;s++)n[0][s]=s;for(i=1;i<=e.length;i++)for(s=1;s<=t.length;s++)e.charAt(i-1)===t.charAt(s-1)?n[i][s]=n[i-1][s-1]:n[i][s]=Math.min(n[i-1][s-1]+1,Math.min(n[i][s-1]+1,n[i-1][s]+1));return n[e.length][t.length]}return t}.apply(e,n),!(void 0!==s&&(t.exports=s))}]);
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