Improve configuration and display of collection operation tools.

client/galaxy/scripts/mvc/tool/tools.js

@@ -521,14 +521,15 @@ var ToolLinkView = BaseView.extend({
         var $link = $('<div/>');
         $link.append(templates.tool_link(this.model.toJSON()));
 
+        var formStyle = this.model.get( 'form_style', null );
         // open upload dialog for upload tool
         if (this.model.id === 'upload1') {
             $link.find('a').on('click', function(e) {
                 e.preventDefault();
                 Galaxy.upload.show();
             });
         }
-        else if ( this.model.get( 'model_class' ) === 'Tool' ) { // regular tools
+        else if ( formStyle === 'regular' ) { // regular tools
             var self = this;
             $link.find('a').on('click', function(e) {
                 e.preventDefault();

config/tool_conf.xml.sample

@@ -30,6 +30,12 @@
   <section id="send" name="Send Data">
     <tool file="genomespace/genomespace_exporter.xml" />
   </section>
+  <section id="collection_operations" name="Collection Operations">
+    <tool file="${model_tools_path}/unzip_collection.xml" />
+    <tool file="${model_tools_path}/zip_collection.xml" />
+    <tool file="${model_tools_path}/filter_failed_collection.xml" />
+    <tool file="${model_tools_path}/flatten_collection.xml" />
+  </section>
   <section id="liftOver" name="Lift-Over">
     <tool file="extract/liftOver_wrapper.xml" />
   </section>

lib/galaxy/tools/__init__.py

@@ -65,6 +65,7 @@
 log = logging.getLogger( __name__ )
 
 HELP_UNINITIALIZED = threading.Lock()
+MODEL_TOOLS_PATH = os.path.dirname(__file__)
 
 
 class ToolErrorLog:
@@ -165,6 +166,11 @@ def get_tool_components( self, tool_id, tool_version=None, get_loaded_tools_by_l
                 break
         return tool_version_select_field, tools, tool
 
+    def _path_template_kwds( self ):
+        return {
+            "model_tools_path": MODEL_TOOLS_PATH,
+        }
+
     def _get_tool_shed_repository( self, tool_shed, name, owner, installed_changeset_revision ):
         # Abstract toolbox doesn't have a dependency on the the database, so
         # override _get_tool_shed_repository here to provide this information.
@@ -1585,6 +1591,10 @@ def to_dict( self, trans, link_details=False, io_details=False ):
 
         tool_dict[ 'panel_section_id' ], tool_dict[ 'panel_section_name' ] = self.get_panel_section()
 
+        tool_class = self.__class__
+        regular_form = tool_class == Tool or isinstance(self, DatabaseOperationTool)
+        tool_dict["form_style"] = "regular" if regular_form else "special"
+
         return tool_dict
 
     def to_json( self, trans, kwd={}, job=None, workflow_building_mode=False ):

lib/galaxy/tools/special_tools.py

@@ -4,10 +4,6 @@
 SPECIAL_TOOLS = {
     "history export": "galaxy/tools/imp_exp/exp_history_to_archive.xml",
     "history import": "galaxy/tools/imp_exp/imp_history_from_archive.xml",
-    "collection unzip": "galaxy/tools/unzip_collection.xml",
-    "collection zip": "galaxy/tools/zip_collection.xml",
-    "filter failed datasets": "galaxy/tools/filter_failed_collection.xml",
-    "flatten collection": "galaxy/tools/flatten_collection.xml",
 }
 
 

lib/galaxy/tools/toolbox/base.py

@@ -539,9 +539,14 @@ def remove_from_dict( has_elems, integrated_has_elems ):
         else:
             remove_from_dict( self._tool_panel, self._integrated_tool_panel )
 
+    def _path_template_kwds( self ):
+        return {}
+
     def _load_tool_tag_set( self, item, panel_dict, integrated_panel_dict, tool_path, load_panel_dict, guid=None, index=None, internal=False ):
         try:
-            path = item.get( "file" )
+            path_template = item.get( "file" )
+            template_kwds = self._path_template_kwds()
+            path = string.Template(path_template).safe_substitute(**template_kwds)
             repository_id = None
 
             tool_shed_repository = None

test/functional/tools/samples_tool_conf.xml

@@ -104,4 +104,12 @@
 
   <tool file="simple_constructs.yml" />
 
+  <!-- Load collection operation tools - I consider these part of the
+       "framework" and they are used to in API tests to test the underlying
+       ToolActions. -->
+  <tool file="${model_tools_path}/unzip_collection.xml" />
+  <tool file="${model_tools_path}/zip_collection.xml" />
+  <tool file="${model_tools_path}/filter_failed_collection.xml" />
+  <tool file="${model_tools_path}/flatten_collection.xml" />
+
 </toolbox>