Add venn diagram

config/plugins/visualizations/venn/config/venn.xml

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+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE visualization SYSTEM "../../visualization.dtd">
+<visualization name="Venn Diagram (Benfred)" regular="True">
+    <description>A javascript library for laying out area proportional venn and euler diagrams hosted at https://github.com/benfred/venn.js.</description>
+    <data_sources>
+        <data_source>
+            <model_class>HistoryDatasetAssociation</model_class>
+            <test type="isinstance" test_attr="datatype" result_type="datatype">tabular.Tabular</test>
+            <test type="isinstance" test_attr="datatype" result_type="datatype">tabular.CSV</test>
+            <to_param param_attr="id">dataset_id</to_param>
+        </data_source>
+    </data_sources>
+    <params>
+        <param type="dataset" var_name_in_template="hda" required="true">dataset_id</param>
+    </params>
+    <entry_point entry_point_type="chart" src="static/script.js" css="static/script.css" func="func"/>
+    <specs>
+        <tag>svg</tag>
+    </specs>
+    <groups>
+        <input>
+            <label>Provide a label</label>
+            <name>key</name>
+            <type>text</type>
+            <placeholder>Data label</placeholder>
+            <value>Data label</value>
+        </input>
+        <input>
+            <label>Column with observations</label>
+            <name>observation</name>
+            <type>data_column</type>
+            <is_label>true</is_label>
+        </input>
+    </groups>
+</visualization>

config/plugins/visualizations/venn/package.json

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+{
+    "name": "visualization",
+    "version": "0.1.0",
+    "keywords": [
+        "galaxy",
+        "visualization"
+    ],
+    "license": "AFL-3.0",
+    "dependencies": {
+        "babel-preset-env": "^1.6.1",
+        "backbone": "^1.3.3",
+        "bootstrap": "^3.3.7",
+        "jquery": "^3.1.1",
+        "parcel-bundler": "^1.4.1",
+        "d3": "^3.4.5"
+    },
+    "scripts": {
+        "build": "parcel build src/script.js -d static"
+    }
+}

config/plugins/visualizations/venn/src/script.js

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+import * as Venn from "./venn";
+import * as d3 from "d3";
+window.d3 = d3;
+var Datasets = window.bundleEntries.chartUtilities.Datasets;
+_.extend(window.bundleEntries || {}, {
+    func: function(options) {
+        var self = this;
+        var separator = '_';
+        function _combinations( current, remaining, results ) {
+            var self = this;
+            _.each( remaining, function( value, index ) {
+                var new_current = current.slice();
+                var new_remaining = remaining.slice();
+                new_remaining.splice( 0, index + 1 );
+                new_current.push( value );
+                results.push( new_current );
+                _combinations( new_current, new_remaining, results );
+            });
+        };
+        Datasets.request({
+            dataset_id      : options.chart.get( 'dataset_id' ),
+            dataset_groups  : options.chart.groups,
+            success         : function( result ) {
+                var group_keys   = [];
+                var group_values = [];
+                var all_values   = {};
+                var set_size     = {};
+                var group_ids    = [];
+                _.each( result, function( group, i ) {
+                    var group_index = {};
+                    _.each( group.values, function( d ) {
+                        all_values[ d.observation ] = group_index[ d.observation ] = true;
+                    });
+                    group_keys.push( group.key );
+                    group_values.push( group_index );
+                    group_ids.push( i );
+                });
+                var combos = [];
+                _combinations( [], group_ids, combos );
+                var sets = [];
+                _.each( combos, function( c ) {
+                    var size = 0;
+                    for ( var value in all_values ) {
+                        var found = 0;
+                        _.each( c, function( group_id ) {
+                            if ( group_values[ group_id ][ value ] ) {
+                                found++;
+                            }
+                        });
+                        if ( found == c.length ) {
+                            size++;
+                        }
+                    }
+                    if ( size > 0 ) {
+                        var set_labels = [];
+                        _.each( c, function( id ) {
+                            set_labels.push( group_keys[ id ]);
+                        });
+                        sets.push( { sets: set_labels, size: size } );
+                    }
+                });
+                var svg = d3.select( '#' + options.targets[ 0 ] ).datum( sets ).call( Venn.VennDiagram() );
+                var tooltip = null;
+                svg.selectAll( 'g' )
+                   .on( 'mouseover', function( d, i ) {
+                        Venn.sortAreas( svg, d );
+                        tooltip = d3.select( 'body' ).append( 'div' ).attr( 'class', 'venntooltip' );
+                        tooltip.transition().duration( 400 ).style( 'opacity', .9 );
+                        tooltip.text(d.size );
+                        var selection = d3.select( this ).transition( 'tooltip' ).duration( 400 );
+                        selection.select( 'path' )
+                                 .style( 'stroke-width', 3 )
+                                 .style( 'fill-opacity', d.sets.length == 1 ? .4 : .1 )
+                                 .style( 'stroke-opacity', 1 );
+                   })
+                   .on( 'mousemove', function() {
+                        tooltip.style( 'left', ( d3.event.pageX ) + 'px')
+                               .style( 'top', ( d3.event.pageY - 28 ) + 'px');
+                   })
+                   .on( 'mouseout', function( d, i ) {
+                        tooltip.remove();
+                   });
+                options.chart.state( 'ok', 'Venn diagram drawn.' );
+                options.process.resolve();
+            }
+        });
+    }
+});