Mercurial > repos > proteore > proteore_venn_diagram

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planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
author proteore
date Sun, 26 Nov 2017 19:09:40 -0500
parents
children 760470ddb9ca
files README.rst jvenn_template.html test-data/DESeq.txt test-data/FQ.txt test-data/RPKM.txt test-data/TC.txt test-data/TMM.txt test-data/UQ.txt test-data/venn_diagram_summary.html test-data/venn_diagram_text_output.txt venn_diagram.py venn_diagram.xml
diffstat 12 files changed, 7051 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.rst	Sun Nov 26 19:09:40 2017 -0500
@@ -0,0 +1,49 @@
+Wrapper for Jvenn plug-in
+=========================
+
+**Authors**
+
+Philippe Bardou, Jérôme Mariette, Frédéric Escudié, Christophe Djemiel and Christophe Klopp. jvenn: an interactive Venn diagram viewer. BMC Bioinformatics 2014, 15:293 doi:10.1186/1471-2105-15-293
+
+**Galaxy integration**
+
+T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR
+
+Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit,Migale Bioinformatics platform
+
+Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool.
+
+=========================
+
+This tool draw a venn diagram from lists/files using Jvenn plug-in (http://jvenn.toulouse.inra.fr/app/index.html). It also creates output files that contain common or specific elements between query and each compared lists/files.
+
+**Inputs**
+
+* **Query file:** A file containing different information of proteins, could be output of previous components.
+
+* **File of a list of IDs:** .TXT format, each line contains 1 ID
+    
+    AMY1A
+    
+ 	ALB
+ 	
+ 	IGKC
+ 	
+ 	CSTA
+ 	
+ 	IGHA1
+ 	
+ 	ACTG1
+
+* **List of IDs:** IDs separated by a space
+    AMY1A ALB IGKC CSTA IGHA1 ACTG1
+
+If you choose a file, it is necessary to specify the column where you would like to perform the comparison.
+
+**Outputs**
+
+* **Summary file** (venn_diagram_summary.html):
+    Venn diagram: Could be downloaded as image (PNG, SVG)
+
+* **Venn text output file**
+    A text file containing common/specific elements among compared lists/files.
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/jvenn_template.html	Sun Nov 26 19:09:40 2017 -0500
@@ -0,0 +1,228 @@
+<!DOCTYPE html>
+<!--
+# Copyright (C) 2015 INRA
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+-->
+<html>
+	<head>
+		<title>Jvenn+</title>
+		<meta charset="UTF-8">
+		<meta name="version" content="2.0.1">
+		<link rel="stylesheet" href="https://cdn.datatables.net/1.10.6/css/jquery.dataTables.css"></link>
+		<link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.4/css/bootstrap.min.css"></link>
+		<style type="text/css">
+			#js-alert {
+				width: 90%;
+				margin-right: auto;
+				margin-left: auto;
+			}
+			#content {
+				width: 90%;
+				margin-right: auto;
+				margin-left: auto;
+			}
+			.clear {
+				clear: both;
+				height: 0px;
+				width: 100%;
+				float: none !important;
+			}
+			ul.nav-tabs {
+				margin-bottom: 30px;
+			}
+			#venn-filters {
+				padding: 10px;
+				background-color: #FFF;
+				background-clip: padding-box;
+				border: 1px solid rgba(0, 0, 0, 0.15);
+				border-radius: 4px;
+				box-shadow: 0px 6px 12px rgba(0, 0, 0, 0.176);
+				margin-right: auto;
+				margin-left: auto;
+				margin-bottom: 30px;
+			}
+			#byFilters-jvenn {
+				margin-right: auto;
+				margin-left: auto;
+			}
+			#venn-filters ul {
+				list-style-type: none;
+			}
+		</style>
+
+		<script type="text/javascript" src="http://code.jquery.com/jquery-2.1.3.min.js"></script>
+		<script type="text/javascript" src="http://code.highcharts.com/4.1.4/highcharts.js"></script>
+		<script type="text/javascript" src="http://code.highcharts.com/4.1.4/modules/exporting.js"></script>
+		<script type="text/javascript" src="https://cdn.datatables.net/1.10.6/js/jquery.dataTables.min.js"></script>
+		<script type="text/javascript" src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.4/js/bootstrap.min.js"></script>
+		<script type="text/javascript">
+			/***************************************************************
+			*  Copyright notice
+			*
+			*  (c) 2014 PF bioinformatique de Toulouse
+			*  All rights reserved
+			* 
+			*
+			*  This script is an adaptation of the venny script developed by
+			*  Juan Carlos Oliveros, BioinfoGP, CNB-CSIC:
+			*  Oliveros, J.C. (2007) VENNY. An interactive tool for comparing 
+			*  lists with Venn Diagrams.
+			*  http://bioinfogp.cnb.csic.es/tools/venny/index.html.
+			*  It is distributed under the terms of the GNU General Public 
+			*  License as published by the Free Software Foundation; either 
+			*  version 2 of the License, or (at your option) any later version.
+			*
+			*  The GNU General Public License can be found at
+			*  http://www.gnu.org/copyleft/gpl.html.
+			*
+			*  This script is distributed in the hope that it will be useful,
+			*  but WITHOUT ANY WARRANTY; without even the implied warranty of
+			*  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+			*  GNU General Public License for more details.
+			*
+			*  This copyright notice MUST APPEAR in all copies of the script!
+			***************************************************************/
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class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC000010"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC110000"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC101000"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC100100"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC100010"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC011000"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC010100"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC010010"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC001100"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC001010"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC000110"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC111000"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC110100"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC110010"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC101100"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC101010"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC100110"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC011100"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC011010"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC010110"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC001110"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC111100"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC111010"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC110110"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC101110"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC011110"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC111110"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC000001"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC000011"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC000101"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC000111"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC001001"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC001011"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC001101"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC001111"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC010001"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC010011"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC010101"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC010111"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC011001"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC011011"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC011101"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC011111"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC100001"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC100011"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC100101"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC100111"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC101001"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC101011"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC101101"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC101111"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC110001"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC110011"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC110101"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC110111"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC111001"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC111011"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC111101"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC111111"></div>',o+='<div style="position: absolute; left: -1000px; top: -1000px; opacity:0.5;" id="label1"></div>',o+='<div style="position: absolute; left: -1000px; top: -1000px; opacity:0.5;" id="label2"></div>',o+='<div style="position: absolute; left: -1000px; top: -1000px; opacity:0.5;" id="label3"></div>',o+='<div style="position: absolute; left: -1000px; top: -1000px; opacity:0.5;" id="label4"></div>',o+='<div style="position: absolute; left: -1000px; top: -1000px; opacity:0.5;" id="label5"></div>',o+='<div style="position: absolute; left: -1000px; top: -1000px; opacity:0.5;" id="label6"></div>',o+="</div>",t.html(o),j=new C2S(O,N),s("*[id^=resultC]").each(function(){s(this).html(0),s(this).addClass("number-empty"),s(this).css("font-size",B.fontSize),s(this).css("font-family",B.fontFamily)}),s("*[id^=label]").each(function(){s(this).css("font-family",B.fontFamily)});var c=z();"list"==c[0]?w():"count"==c[0]&&E(),null!=B.searchInput&&B.searchInput.keyup(function(){F(B.searchInput.val(),B.searchMinSize)}),"edwards"==B.displayMode?y(c[1]):x(c[1]),B.displayStat&&v(c[1]),B.exporting===!0&&S(t,e,c[0]),c[1]>=4&&_(t,c[1]),s(".number-black").hover(function(){var t=!1;s("*[id^=item]").each(function(){"on"===s(this).children("span").text()&&(t=!0)});var e=!1;if(null!=B.searchInput&&""!=B.searchInput.val()&&(e=!0),!t&&!e&&""!==s(this).text()){var l=this.listnames,r=this;s("*[id^=label]").each(function(){l.indexOf(s(this).text())<0?s(this).css("opacity",.1):s(this).css("opacity",.6)}),s(".number-black").each(function(){this!=r&&s(this).css("opacity",.1)}),b(),"edwards"==B.displayMode?y(c[1]):x(c[1]),B.displayStat&&v(c[1])}},function(){var t=!1;s("*[id^=item]").each(function(){"on"===s(this).children("span").text()&&(t=!0)});var e=!1;if(null!=B.searchInput&&""!=B.searchInput.val()&&(e=!0),!t&&!e&&""!==s(this).text()){{this.listnames}s("*[id^=label]").each(function(){s(this).css("opacity",.5)}),s(".number-black").each(function(){s(this).css("opacity",1)}),b(),"edwards"==B.displayMode?y(c[1]):x(c[1]),B.displayStat&&v(c[1])}}),s("#canvasEllipse").html(j.getSvg())}),this}}(jQuery);
+		</script>
+		<script type="text/javascript">
+			/*
+			 * HTMLTable.js 0.1.0 - HTMLTable Library
+			 *
+			 * Copyright (c) 2015 Escudie Frederic
+			 * Licensed under the MIT (http://www.opensource.org/licenses/mit-license.php) license.
+			 */
+			function HTMLtable(e){var t,r,n=e,a=";";this.deleteColumns=function(e){for(var a=n.getElementsByTagName("tr"),o=0;o<a.length;o++){s=0;var i=a[o].getElementsByTagName("td");0==i.length&&(i=a[o].getElementsByTagName("th"));for(var v=0,s=0;s<t[1];s++)if(!r[o][s]){var f=i[v].getAttribute("colspan");if(null!=f)for(var m=0;f>m;m++){if(in_array(s+m,e)){var u=i[v].getAttribute("colspan");u-1==0?i[v].removeAttribute("colspan"):i[v].setAttribute("colspan",u-1)}if(null==i[v].getAttribute("colspan")){var h=i[v];a[o].removeChild(h),v--}}else if(in_array(s,e)){var h=i[v];a[o].removeChild(h),v--}v++}}l(),g()},this.filter=function(e,a){var l=new RegExp(e),g=new Array;null!=a&&a||(g.c0=!0);for(var o=n.getElementsByTagName("tr"),i=0;i<o.length;i++){f=0;var v=o[i].getElementsByTagName("td");if(0!=v.length)for(var s=0,f=0;f<t[1];f++)r[i][f]||(l.test(v[s].innerHTML)&&(g["c"+f]=!0),s++)}for(var m=new Array,u=0;u<t[1];u++)void 0===g["c"+u]&&m.push(u);this.deleteColumns(m)},this.getModel=function(){return n};var l=function(){for(var e=0,r=0,a=n.getElementsByTagName("tr"),l=0;l<a.length;l++){var g=0;e++;var o=a[l].getElementsByTagName("td");0==o.length&&(o=a[l].getElementsByTagName("th"));for(var i=0;i<o.length;i++){var v=o[i].getAttribute("colspan");g+=null==v?1:parseInt(v)}g>r&&(r=g)}t=new Array(2),t[0]=e,t[1]=r},g=function(){r=new Array(t[0]);for(var e=0;e<t[0];e++){r[e]=new Array(t[1]);for(var a=0;a<t[1];a++)r[e][a]=!1}for(var l=n.getElementsByTagName("tr"),g=0;g<l.length;g++){v=0;var o=l[g].getElementsByTagName("td");0==o.length&&(o=l[g].getElementsByTagName("th"));for(var i=0,v=0;v<t[1];v++)if(!r[g][v]){var s=0,f=0,m=o[i].getAttribute("rowspan");null!=m&&(s=parseInt(m)-1);var u=o[i].getAttribute("colspan");null!=u&&(f=parseInt(u)-1);for(var h=s;h>=0;h--)for(var y=f;y>=0;y--)(0!=h||0!=y)&&(r[g+h][v+y]=!0);i++}}};this.replace=function(e,a,l){var g=new RegExp(e);null==a&&(a=""),null==l&&(l="");for(var o=n.getElementsByTagName("tr"),i=0;i<o.length;i++){f=0;var v=o[i].getElementsByTagName("td");if(0!=v.length)for(var s=0,f=0;f<t[1];f++)if(!r[i][f]){var m=g.exec(v[s].innerHTML);null!=m&&(void 0===m[1]&&(m[1]=""),v[s].innerHTML=a+m[1]+l),s++}}},this.toCSV=function(){for(var e="",l=n.getElementsByTagName("tr"),g=0;g<l.length;g++){var o=l[g].getElementsByTagName("td");0==o.length&&(o=l[g].getElementsByTagName("th"));for(var i=0,v=0;v<t[1];v++)r[g][v]||(e+=o[i].innerHTML,i++),e+=a;e=e.substr(0,e.length-1)+"\n"}return e},l(),g()}var in_array=function(e,t){for(var r in t)if(t[r]==e)return!0;return!1};
+			
+			/*
+			 * dataTableExtractor.plugin.js 0.1.0 - datatableExport Library
+			 *
+			 * Copyright (c) 2015 Escudie Frederic
+			 * Licensed under the MIT (http://www.opensource.org/licenses/mit-license.php) license.
+			 */
+			!function(t){t.fn.datatableExport=function(a){var e={anchor_id:t(this).attr("id"),table_id:null,csv_separator:";",omitted_columns:[]},n=t.extend(e,a);if(!t(this).length)throw"The element where the datatableExport is called does not exist.";if(void 0==n.anchor_id)throw"The datatableExport plugin must be called on an element with id.";if(null==n.table_id)throw"You must set the table_id parameter in datatableExport plugin.";if(!t("#"+n.table_id))throw"The datatable '#"+n.table_id+"' cannot be retieve in DOM.";return this.each(function(){var a=t(this);a.on("click",function(){t.fn.datatableExport.csv(n.anchor_id,n.table_id,n.csv_separator,n.omitted_columns)})})},t.fn.datatableExport.cleanCellMarkup=function(a,e){t.parseHTML(e);t("#"+a).append('<div class="hidden data-tmp">'+e+"</div>"),t("#"+a+" .data-tmp").find("input").each(function(){var a="";a=t(this).is(":checkbox")?t(this).is(":checked")?"true":"false":t(this).val(),t(this).replaceWith(a)});var n=t("#"+a+" .data-tmp").text();return t("#"+a+" .data-tmp").remove(),n},t.fn.datatableExport.csv=function(a,e,n,i){var l="",r=t("#"+e).DataTable(),d=t("#"+e+" thead")[0],o=new HTMLtable(d.cloneNode(!0));o.deleteColumns(i),l+=o.toCSV();var c=r.rows().data();t.each(c,function(e,n){for(var r="",d=0;d<n.length;d++)-1==t.inArray(d,i)&&(r+='"'+t.fn.datatableExport.cleanCellMarkup(a,n[d])+'";');""!=r&&(r=r.slice(0,-1)),l+=r+"\n"}),t("#"+a+"-extract-csv").length||t("#"+a).append('<a id="'+a+'-extract-csv" href="data:text/csv;charset=UTF-8,'+encodeURI(l)+'" download="data.csv" style="display:none;"></a>'),t("#"+a+"-extract-csv")[0].click()}}(jQuery);
+		</script>		
+		
+		<script type="text/javascript">
+/*
+$(document).ready(function(){
+  $('#example').jvenn({
+    series: [{
+    	name: {A: 'Actors',
+               B: 'Singers'},
+    	data: {A: ["Arnold Schwarzenegger", "Jack Nicholson", "Robert de Niro", "Harrison Ford"], B: ["Freddy Mercury", "Ricky Martin", "Celine Dion"], AB: ["Marilyn Monroe", "Barbra Streisand", "Dean Martin"]},
+    	values: {A: 4, B: 3, AB: 3}
+    }],
+  });
+});
+*/
+var jvenn_data = ###JVENN_DATA### ;
+$(document).ready(function(){
+  $('#example').jvenn(jvenn_data);
+});
+
+			///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
+			//
+			// Data
+			//
+			///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
+			//var processed_filters = ###PORCESSED_FILTERS### ;
+			/* Example:
+				['filterA', 'filterB', 'filterC']
+			*/
+			//var global_results = ###GLOBAL_RESULTS### ; 
+			/* Example: 
+				{
+					'nb_clstr_kept': 100,
+					'nb_clstr_ini': 300,
+					'nb_seq_kept': 100,
+					'nb_seq_ini': 100000
+				}
+			*/
+			//var by_samples_results = ###SAMPLES_RESULTS### ;
+			/* Example:
+				{
+					'sampleA':{
+						'filtered':{
+							'filterA': 10,
+							'filterB': 20
+						},
+						'initial': 75,
+						'kept': 50
+					},
+					'sampleB':{
+						'filtered':{
+							'filterB': 20,
+						},
+						'initial': 110,
+						'kept': 90
+					}
+				}
+			*/
+			//var by_filters_results = ###FILTERS_RESULTS### ;
+			/* Example:
+				[
+					{'filters':['filterA'], 'count': 10},
+					{'filters':['filterB'], 'count': 20},
+					{'filters':['filterC'], 'count': 30},
+					{'filters':['filterA', 'filterB'], 'count': 1},
+					{'filters':['filterA', 'filterC'], 'count': 2},
+					{'filters':['filterB', 'filterC'], 'count': 3},
+					{'filters':['filterA', 'filterB', 'filterC'], 'count': 4}
+				];
+			*/
+			
+			///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
+			//
+			// Main
+			//
+			///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
+			$(function() {
+				// Remove alert
+				$('#js-alert').remove();
+				$('#content').removeClass("hidden");
+				
+				// Load active tab
+				global_filters_load();
+				intersections_filters_load();
+				
+				// Add tab listener
+				$('.nav-tabs a').click(function (e) {
+					e.preventDefault();
+					$(this).tab('show');
+					if( $(this).attr('href') == "#view-by-samples" && $('#view-by-samples').hasClass('disabled') ){
+						$('#view-by-samples').removeClass('disabled')
+						samples_filters_load( "filter-log" );
+					}
+				})
+			});
+		</script>
+
+	</head>
+	<body>
+		<!-- Alert -->
+		<p id="js-alert" class="alert alert-warning">
+                javascript is needed to display data.<br />
+                If you try to view this data on galaxy please contact your administrator to authorise javascript or download the file to view.
+		</p>
+		
+        <!-- Content -->
+	<div id="example"></div>
+        </div>
+
+		
+	</body>
+</html>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/DESeq.txt	Sun Nov 26 19:09:40 2017 -0500
@@ -0,0 +1,1249 @@
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+G000318
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+G000635
+G000637
+G000646
+G000655
+G000660
+G000663
+G000665
+G000668
+G000669
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/FQ.txt	Sun Nov 26 19:09:40 2017 -0500
@@ -0,0 +1,1092 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/RPKM.txt	Sun Nov 26 19:09:40 2017 -0500
@@ -0,0 +1,417 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/TC.txt	Sun Nov 26 19:09:40 2017 -0500
@@ -0,0 +1,548 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/TMM.txt	Sun Nov 26 19:09:40 2017 -0500
@@ -0,0 +1,1190 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/UQ.txt	Sun Nov 26 19:09:40 2017 -0500
@@ -0,0 +1,1213 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/venn_diagram_summary.html	Sun Nov 26 19:09:40 2017 -0500
@@ -0,0 +1,228 @@
+<!DOCTYPE html>
+<!--
+# Copyright (C) 2015 INRA
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+-->
+<html>
+	<head>
+		<title>Jvenn+</title>
+		<meta charset="UTF-8">
+		<meta name="version" content="2.0.1">
+		<link rel="stylesheet" href="https://cdn.datatables.net/1.10.6/css/jquery.dataTables.css"></link>
+		<link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.4/css/bootstrap.min.css"></link>
+		<style type="text/css">
+			#js-alert {
+				width: 90%;
+				margin-right: auto;
+				margin-left: auto;
+			}
+			#content {
+				width: 90%;
+				margin-right: auto;
+				margin-left: auto;
+			}
+			.clear {
+				clear: both;
+				height: 0px;
+				width: 100%;
+				float: none !important;
+			}
+			ul.nav-tabs {
+				margin-bottom: 30px;
+			}
+			#venn-filters {
+				padding: 10px;
+				background-color: #FFF;
+				background-clip: padding-box;
+				border: 1px solid rgba(0, 0, 0, 0.15);
+				border-radius: 4px;
+				box-shadow: 0px 6px 12px rgba(0, 0, 0, 0.176);
+				margin-right: auto;
+				margin-left: auto;
+				margin-bottom: 30px;
+			}
+			#byFilters-jvenn {
+				margin-right: auto;
+				margin-left: auto;
+			}
+			#venn-filters ul {
+				list-style-type: none;
+			}
+		</style>
+
+		<script type="text/javascript" src="http://code.jquery.com/jquery-2.1.3.min.js"></script>
+		<script type="text/javascript" src="http://code.highcharts.com/4.1.4/highcharts.js"></script>
+		<script type="text/javascript" src="http://code.highcharts.com/4.1.4/modules/exporting.js"></script>
+		<script type="text/javascript" src="https://cdn.datatables.net/1.10.6/js/jquery.dataTables.min.js"></script>
+		<script type="text/javascript" src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.4/js/bootstrap.min.js"></script>
+		<script type="text/javascript">
+			/***************************************************************
+			*  Copyright notice
+			*
+			*  (c) 2014 PF bioinformatique de Toulouse
+			*  All rights reserved
+			* 
+			*
+			*  This script is an adaptation of the venny script developed by
+			*  Juan Carlos Oliveros, BioinfoGP, CNB-CSIC:
+			*  Oliveros, J.C. (2007) VENNY. An interactive tool for comparing 
+			*  lists with Venn Diagrams.
+			*  http://bioinfogp.cnb.csic.es/tools/venny/index.html.
+			*  It is distributed under the terms of the GNU General Public 
+			*  License as published by the Free Software Foundation; either 
+			*  version 2 of the License, or (at your option) any later version.
+			*
+			*  The GNU General Public License can be found at
+			*  http://www.gnu.org/copyleft/gpl.html.
+			*
+			*  This script is distributed in the hope that it will be useful,
+			*  but WITHOUT ANY WARRANTY; without even the implied warranty of
+			*  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+			*  GNU General Public License for more details.
+			*
+			*  This copyright notice MUST APPEAR in all copies of the script!
+			***************************************************************/
+			!function(){"use strict";function s(s,t){var e,l=Object.keys(t);for(e=0;e<l.length;e++)s=s.replace(new RegExp("\\{"+l[e]+"\\}","gi"),t[l[e]]);return s}function t(s){var t,e,l;if(!s)throw new Error("cannot create a random attribute name for an undefined object");t="ABCDEFGHIJKLMNOPQRSTUVWXTZabcdefghiklmnopqrstuvwxyz",e="";do for(e="",l=0;12>l;l++)e+=t[Math.floor(Math.random()*t.length)];while(s[e]);return e}function e(s,t){var e,l,r,o={};for(s=s.split(","),t=t||10,e=0;e<s.length;e+=2)l="&"+s[e+1]+";",r=parseInt(s[e],t),o[l]="&#"+r+";";return o["\\xa0"]="&#160;",o}function l(s){var t={left:"start",right:"end",center:"middle",start:"start",end:"end"};return t[s]||t.start}function r(s){var t={alphabetic:"alphabetic",hanging:"hanging",top:"text-before-edge",bottom:"text-after-edge",middle:"central"};return t[s]||t.alphabetic}var 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+		</script>
+		<script type="text/javascript">
+			/*
+			 * HTMLTable.js 0.1.0 - HTMLTable Library
+			 *
+			 * Copyright (c) 2015 Escudie Frederic
+			 * Licensed under the MIT (http://www.opensource.org/licenses/mit-license.php) license.
+			 */
+			function HTMLtable(e){var t,r,n=e,a=";";this.deleteColumns=function(e){for(var a=n.getElementsByTagName("tr"),o=0;o<a.length;o++){s=0;var i=a[o].getElementsByTagName("td");0==i.length&&(i=a[o].getElementsByTagName("th"));for(var v=0,s=0;s<t[1];s++)if(!r[o][s]){var f=i[v].getAttribute("colspan");if(null!=f)for(var m=0;f>m;m++){if(in_array(s+m,e)){var u=i[v].getAttribute("colspan");u-1==0?i[v].removeAttribute("colspan"):i[v].setAttribute("colspan",u-1)}if(null==i[v].getAttribute("colspan")){var h=i[v];a[o].removeChild(h),v--}}else if(in_array(s,e)){var h=i[v];a[o].removeChild(h),v--}v++}}l(),g()},this.filter=function(e,a){var l=new RegExp(e),g=new Array;null!=a&&a||(g.c0=!0);for(var o=n.getElementsByTagName("tr"),i=0;i<o.length;i++){f=0;var v=o[i].getElementsByTagName("td");if(0!=v.length)for(var s=0,f=0;f<t[1];f++)r[i][f]||(l.test(v[s].innerHTML)&&(g["c"+f]=!0),s++)}for(var m=new Array,u=0;u<t[1];u++)void 0===g["c"+u]&&m.push(u);this.deleteColumns(m)},this.getModel=function(){return n};var l=function(){for(var e=0,r=0,a=n.getElementsByTagName("tr"),l=0;l<a.length;l++){var g=0;e++;var o=a[l].getElementsByTagName("td");0==o.length&&(o=a[l].getElementsByTagName("th"));for(var i=0;i<o.length;i++){var v=o[i].getAttribute("colspan");g+=null==v?1:parseInt(v)}g>r&&(r=g)}t=new Array(2),t[0]=e,t[1]=r},g=function(){r=new Array(t[0]);for(var e=0;e<t[0];e++){r[e]=new Array(t[1]);for(var a=0;a<t[1];a++)r[e][a]=!1}for(var l=n.getElementsByTagName("tr"),g=0;g<l.length;g++){v=0;var o=l[g].getElementsByTagName("td");0==o.length&&(o=l[g].getElementsByTagName("th"));for(var i=0,v=0;v<t[1];v++)if(!r[g][v]){var s=0,f=0,m=o[i].getAttribute("rowspan");null!=m&&(s=parseInt(m)-1);var u=o[i].getAttribute("colspan");null!=u&&(f=parseInt(u)-1);for(var h=s;h>=0;h--)for(var y=f;y>=0;y--)(0!=h||0!=y)&&(r[g+h][v+y]=!0);i++}}};this.replace=function(e,a,l){var g=new RegExp(e);null==a&&(a=""),null==l&&(l="");for(var o=n.getElementsByTagName("tr"),i=0;i<o.length;i++){f=0;var v=o[i].getElementsByTagName("td");if(0!=v.length)for(var s=0,f=0;f<t[1];f++)if(!r[i][f]){var m=g.exec(v[s].innerHTML);null!=m&&(void 0===m[1]&&(m[1]=""),v[s].innerHTML=a+m[1]+l),s++}}},this.toCSV=function(){for(var e="",l=n.getElementsByTagName("tr"),g=0;g<l.length;g++){var o=l[g].getElementsByTagName("td");0==o.length&&(o=l[g].getElementsByTagName("th"));for(var i=0,v=0;v<t[1];v++)r[g][v]||(e+=o[i].innerHTML,i++),e+=a;e=e.substr(0,e.length-1)+"\n"}return e},l(),g()}var in_array=function(e,t){for(var r in t)if(t[r]==e)return!0;return!1};
+			
+			/*
+			 * dataTableExtractor.plugin.js 0.1.0 - datatableExport Library
+			 *
+			 * Copyright (c) 2015 Escudie Frederic
+			 * Licensed under the MIT (http://www.opensource.org/licenses/mit-license.php) license.
+			 */
+			!function(t){t.fn.datatableExport=function(a){var e={anchor_id:t(this).attr("id"),table_id:null,csv_separator:";",omitted_columns:[]},n=t.extend(e,a);if(!t(this).length)throw"The element where the datatableExport is called does not exist.";if(void 0==n.anchor_id)throw"The datatableExport plugin must be called on an element with id.";if(null==n.table_id)throw"You must set the table_id parameter in datatableExport plugin.";if(!t("#"+n.table_id))throw"The datatable '#"+n.table_id+"' cannot be retieve in DOM.";return this.each(function(){var a=t(this);a.on("click",function(){t.fn.datatableExport.csv(n.anchor_id,n.table_id,n.csv_separator,n.omitted_columns)})})},t.fn.datatableExport.cleanCellMarkup=function(a,e){t.parseHTML(e);t("#"+a).append('<div class="hidden data-tmp">'+e+"</div>"),t("#"+a+" .data-tmp").find("input").each(function(){var a="";a=t(this).is(":checkbox")?t(this).is(":checked")?"true":"false":t(this).val(),t(this).replaceWith(a)});var n=t("#"+a+" .data-tmp").text();return t("#"+a+" .data-tmp").remove(),n},t.fn.datatableExport.csv=function(a,e,n,i){var l="",r=t("#"+e).DataTable(),d=t("#"+e+" thead")[0],o=new HTMLtable(d.cloneNode(!0));o.deleteColumns(i),l+=o.toCSV();var c=r.rows().data();t.each(c,function(e,n){for(var r="",d=0;d<n.length;d++)-1==t.inArray(d,i)&&(r+='"'+t.fn.datatableExport.cleanCellMarkup(a,n[d])+'";');""!=r&&(r=r.slice(0,-1)),l+=r+"\n"}),t("#"+a+"-extract-csv").length||t("#"+a).append('<a id="'+a+'-extract-csv" href="data:text/csv;charset=UTF-8,'+encodeURI(l)+'" download="data.csv" style="display:none;"></a>'),t("#"+a+"-extract-csv")[0].click()}}(jQuery);
+		</script>		
+		
+		<script type="text/javascript">
+/*
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"G002118", "G004726", "G002059", "G005217", "G005215", "G003904", "G001215", "G004786", "G004222", "G001528", "G004561", "G003020", "G004682", "G003344", "G000242", "G004355", "G004356"], "AE": ["G000080", "G004384", "G002405", "G003427", "G004700", "G002541", "G004994", "G003751", "G004667", "G004089", "G002905", "G002841", "G001451"], "ABCE": [], "DEF": [], "AD": [], "BCDE": [], "CEF": [], "BCDF": [], "ABCF": [], "AF": ["G001203", "G004708", "G003149", "G002637", "G001114", "G002037"], "ABC": [], "BCDEF": ["G005214"], "BCD": ["G002462"], "ADEF": ["G001285", "G002062"], "ABDEF": ["G001197", "G001193", "G001052", "G003936", "G003838", "G004554", "G000391", "G002234", "G002237", "G001985", "G002131", "G003232", "G002336", "G004206", "G003729", "G002912", "G000026", "G000236", "G004365", "G004473", "G002224", "G003390", "G001184", "G004492", "G001469", "G000318", "G004537", "G000751", "G004389", "G003240", "G000706", "G004061", "G004276", "G003153", "G001874", "G003089", "G002922", "G002895", "G003794", "G005021", "G004863", "G005023", "G000365", "G004009", "G001883", "G002310", "G000605", "G003709", "G004556", "G003014", "G004262", "G002780", "G002392", "G001483", "G002893", "G005138", "G000276", "G001160", "G002362", "G001901", "G001647", "G001567", "G003269", "G003570", "G003576", "G002796", "G003678", "G004151", "G004086", "G002880", "G002886", "G001550", "G002888", "G004749", "G002966", "G000669", "G001794", "G000663", "G004438", "G004478", "G004431", "G001724", "G004733", "G003760", "G002767", "G003078", "G003077", "G002582", "G004753", "G002874", "G000256", "G001785", "G000716", "G000493", "G000805", "G003699", "G002343", "G004394", "G003362", "G001831", "G003368", "G004424", "G005044", "G002775", "G003596", "G001934", "G004213", "G001732", "G001737", "G002191", "G001534", "G002195", "G002215", "G001634", "G001635", "G000832", "G003625", "G002288", "G000082", "G001888", "G003359", "G000931", "G004693", "G002690", "G005050", "G005053", "G003218", "G003219", "G001333", "G002056", "G003746", "G001026", "G001219", "G000431", "G000167", "G001609", "G002206", "G004445", "G002750", "G003340", "G001629", "G004350", "G002901", "G002187", "G002510", "G002040"], "ABEF": ["G001344", "G004551", "G001597", "G000748", "G000620", "G000628", "G000629", "G001296", "G003031", "G001726", "G002038", "G002032", "G001687", "G002526", "G001465", "G004491", "G004144", "G001665", "G001668", "G004467", "G002650", "G004462", "G000845", "G004547", "G002146", "G002624", "G002625", "G002620", "G004648", "G004860", "G000362", "G004643", "G004795", "G004334", "G003661", "G000218", "G003143", "G003928", "G001169", "G000273", "G003110", "G001893", "G001895", "G001897", "G004814", "G002085", "G002245", "G002246", "G002242", "G002715", "G005148", "G005149", "G000444", "G005142", "G004729", "G004082", "G002882", "G002881", "G000788", "G001306", "G000668", "G000540", "G001090", "G000646", "G003446", "G001393", "G004885", "G002402", "G002401", "G000231", "G000144", "G001001", "G002913", "G005033", "G001949", "G002814", "G001944", "G002816", "G001766", "G001940", "G002760", "G001542", "G002585", "G001232", "G002589", "G001628", "G003695", "G001626", "G002007", "G004421", "G002061", "G003043", "G002107", "G003044", "G002104", "G004191", "G003915", "G001434", "G001433", "G004699", "G004698", "G004695", "G004697", "G003183", "G002613", "G002612", "G004458", "G004104", "G004850", "G004593", "G002436", "G005274", "G002200", "G003980", "G003823", "G002209", "G001997", "G001991", "G000982", "G004604", "G003139", "G003138", "G000323", "G004982", "G000116", "G005002", "G005001", "G003522", "G001146", "G001906", "G002446", "G002444", "G000022", "G000023", "G000027", "G000181", "G000180", "G005178", "G000186", "G001278", "G001279", "G001374", "G001379", "G001271", "G004108", "G000759", "G000612", "G005091", "G003411", "G000754", "G002535", "G004972", "G002380", "G002929", "G001972", "G001878", "G001970", "G001877", "G001697", "G001694", "G001978", "G001474", "G004481", "G001478", "G004484", "G004485", "G003381", "G001579", "G004999", "G000976", "G000879", "G004411", "G004410", "G000872", "G003099", "G002655", "G002654", "G004328", "G000274", "G004325", "G004635", "G000270", "G004439", "G003179", "G003953", "G003776", "G003898", "G003956", "G003770", "G003892", "G000203", "G003670", "G004520", "G004745", "G004743", "G004740", "G001155", "G005121", "G004021", "G005231", "G004730", "G005234", "G002996", "G005237", "G000475", "G003818", "G002879", "G002878", "G001707", "G000790", "G004867", "G000497", "G005196", "G005199", "G000498", "G002470", "G001836", "G001385", "G001015", "G002774", "G001937", "G001201", "G002599", "G000834", "G003057", "G002694", "G003588", "G002973", "G002970", "G002979", "G003906", "G003903", "G000988", "G000909", "G002183", "G003637", "G004568", "G000904", "G003733", "G002609", "G003227", "G002184", "G004704", "G003836", "G000232", "G000338", "G000339", "G003643", "G004203", "G000238", "G003649", "G003648", "G004014", "G000041", "G004011", "G001802", "G000194", "G002734", "G003199", "G002301", "G002303", "G000427", "G001119", "G000584", "G001116", "G001110", "G001854", "G002942", "G002941", "G003784", "G004944", "G004947", "G003013", "G003542", "G001809", "G001960", "G001746", "G001749", "G002838", "G001968", "G002391", "G001645", "G001644", "G001646", "G000944", "G003306", "G003302", "G004404", "G004892", "G003261", "G003308", "G001244", "G001241", "G003286", "G000268", "G003282", "G003281", "G004237", "G000261", "G005172", "G005173", "G003160", "G001121", "G004123", "G000404", "G003766", "G004120", "G004539", "G004243", "G003601", "G000890", "G000896", "G000894", "G005118", "G004059", "G000002", "G005114", "G000411", "G002348", "G005073", "G002344", "G004832", "G002341", "G000098", "G003116", "G000301", "G004332", "G004331", "G005204", "G000466", "G005200", "G002868", "G002865", "G002860", "G002863", "G003500", "G003503", "G002194", "G002714", "G005182", "G000526", "G000524", "G004883", "G002464", "G002469", "G002749", "G001929", "G005220", "G004088", "G001022", "G001604", "G001355", "G001606", "G001353", "G001210", "G004302", "G000637", "G000635", "G000631", "G000737", "G000827", "G000730", "G002120", "G003025", "G003342", "G002687", "G001289", "G001324", "G001325", "G001281", "G003938", "G004022", "G003931", "G003163", "G001517", "G001457", "G002051", "G003233", "G003791", "G003238", "G003480", "G003337", "G004470", "G004610", "G000358", "G003800", "G004657", "G004874", "G003808", "G000352", "G004625", "G002228", "G001711", "G004784", "G004377", "G004007", "G001179", "G000078", "G000660", "G004392", "G002096", "G004398", "G002093", "G005227", "G002705", "G002251", "G001108", "G000592", "G001756", "G000772", "G001825", "G002891", "G002439", "G002489", "G002484", "G002957", "G003474", "G002388", "G001083", "G001080", "G002555", "G001394", "G002843", "G001952", "G001073", "G001810", "G001812", "G001776", "G002414", "G002417", "G001227", "G001495", "G001559", "G000468", "G000810", "G000709", "G002671", "G003375", "G004435", "G003076", "G003296", "G000253", "G004220", "G000254", "G001424", "G003949", "G002458", "G000929", "G000927", "G001578", "G004137", "G004501", "G003612", "G004245", "G003201", "G003972", "G004989", "G004988", "G004755", "G004040", "G000405", "G005265", "G004044", "G004980", "G004829", "G002213", "G004290", "G003850", "G004346", "G000317", "G001049", "G003701", "G003538", "G000530", "G000534", "G004535", "G002757", "G002459", "G001910", "G002751", "G002758", "G002320", "G000031", "G001032"], "BDEF": ["G004118"], "A": ["G001905", "G000130", "G000349", "G002946", "G004042", "G002598", "G002420", "G002190", "G004395", "G000389", "G001410", "G000053", "G000189", "G001293", "G001291", "G003379", "G002906", "G000222", "G003407", "G003764", "G002974", "G003644", "G002782", "G002172", "G002079", "G003965", "G000773", "G004036", "G001047", "G004140", "G004711", "G000880", "G004716", "G003934", "G003416", "G004838", "G002205", "G002365", "G004085", "G003453", "G003681", "G001788", "G002084", "G001421", "G003174", "G003630", "G002752", "G004453", "G003690", "G004978", "G002192", "G003433", "G003739", "G003598", "G004208", "G003498", "G001071", "G002640", "G004526", "G000200", "G003425", "G003490", "G002287"], "ACEF": [], "C": [], "B": ["G004580", "G001204", "G002864", "G002803", "G003997", "G001436", "G005184", "G003688", "G000569", "G003544", "G001298", "G004121", "G005031", "G001761", "G004037", "G005014", "G001485", "G004679", "G000570", "G000881", "G001563", "G003758", "G001696", "G004115"], "E": [], "D": [], "ABF": ["G000655", "G004703", "G000046"], "F": ["G003283", "G002316", "G000950", "G001094", "G000919", "G003033", "G003401", "G003940", "G003662", "G002781", "G003484", "G001580", "G002176", "G004364", "G005211", "G005018", "G004659", "G004637", "G001481", "G002220", "G000718", "G000731", "G003851", "G001387", "G002455", "G001139", "G003155"], "ABCDE": [], "EF": ["G001936", "G004930", "G004238", "G000875", "G001275", "G002311", "G003088", "G001657", "G003943", "G001072", "G001509", "G002635", "G000309", "G000471", "G004081"], "ABD": [], "CF": [], "CE": [], "CD": [], "ADF": [], "ADE": [], "ABDE": [], "ACDF": [], "BDF": [], "ABDF": [], "ACDEF": ["G005180"], "ABCDEF": ["G001598", "G000305", "G001343", "G000749", "G005089", "G004967", "G003403", "G001725", "G001729", "G001467", "G001461", "G005250", "G000962", "G000966", "G004096", "G001507", "G004466", "G004543", "G004469", "G003080", "G002628", "G002626", "G003322", "G004649", "G004793", "G004260", "G003142", "G003881", "G004034", "G002899", "G005131", "G000061", "G001890", "G001891", "G002361", "G001899", "G002369", "G002368", "G003041", "G002710", "G002711", "G005222", "G000447", "G002969", "G002968", "G002885", "G000783", "G002967", "G000547", "G001093", "G000665", "G004887", "G002569", "G001820", "G004922", "G004925", "G000147", "G001007", "G001751", "G001760", "G001765", "G001547", "G000714", "G000715", "G000717", "G001780", "G000711", "G001623", "G001620", "G004428", "G003366", "G004907", "G003593", "G003592", "G002101", "G003594", "G004192", "G003919", "G004210", "G003912", "G001539", "G001431", "G003589", "G000934", "G003628", "G002616", "G002610", "G003962", "G003747", "G003964", "G004856", "G004671", "G004992", "G005276", "G004772", "G005273", "G002202", "G003828", "G001998", "G001995", "G001993", "G004351", "G004353", "G000985", "G000984", "G000987", "G002416", "G001283", "G001226", "G001051", "G001053", "G002722", "G001904", "G002331", "G002332", "G002333", "G001123", "G005176", "G005175", "G000028", "G000029", "G000185", "G005094", "G005095", "G002533", "G003558", "G003550", "G001753", "G001976", "G001975", "G002385", "G002384", "G002024", "G001791", "G003388", "G004487", "G004468", "G001575", "G004558", "G001218", "G003093", "G002658", "G002153", "G003315", "G003317", "G004329", "G000420", "G004324", "G001409", "G003177", "G004258", "G000012", "G005126", "G002373", "G000381", "G000376", "G000377", "G004735", "G001704", "G001703", "G003511", "G005192", "G000490", "G005198", "G002475", "G004932", "G004934", "G005043", "G002779", "G002594", "G002595", "G000721", "G000720", "G000725", "G000726", "G001630", "G000728", "G002981", "G001633", "G001288", "G002693", "G002691", "G003059", "G002050", "G002053", "G002975", "G002055", "G002054", "G001840", "G003905", "G003901", "G004161", "G004160", "G001328", "G003634", "G000902", "G003229", "G004119", "G002601", "G004113", "G003222", "G005248", "G005241", "G005243", "G001983", "G002231", "G001987", "G003645", "G000237", "G003125", "G005019", "G000514", "G001061", "G001189", "G000165", "G000696", "G002309", "G000195", "G001386", "G000426", "G004064", "G001115", "G005169", "G000581", "G000517", "G001112", "G002497", "G001362", "G001360", "G003464", "G002011", "G003619", "G003543", "G002833", "G002784", "G002834", "G001748", "G001640", "G001560", "G001565", "G003304", "G003305", "G003865", "G002648", "G004578", "G001247", "G002641", "G004589", "G004623", "G000262", "G001649", "G000899", "G005266", "G003948", "G004241", "G004532", "G000008", "G000009", "G000418", "G000412", "G002928", "G002267", "G003843", "G003847", "G002346", "G000302", "G003113", "G000306", "G004330", "G005201", "G005203", "G005202", "G001736", "G003502", "G005188", "G002199", "G005185", "G005055", "G002297", "G000356", "G001926", "G001605", "G001352", "G001351", "G001359", "G002998", "G002992", "G003023", "G002682", "G002902", "G002048", "G002044", "G001287", "G004170", "G003230", "G004577", "G000857", "G000851", "G004479", "G003486", "G004471", "G002972", "G004475", "G004477", "G004718", "G004307", "G000355", "G004712", "G004713", "G004714", "G004715", "G004783", "G004273", "G004373", "G003154", "G004004", "G005024", "G001171", "G000177", "G001880", "G001889", "G002709", "G002254", "G002383", "G002702", "G005254", "G005255", "G005159", "G004099", "G001102", "G005154", "G004095", "G001107", "G001105", "G002894", "G001319", "G002896", "G002488", "G001317", "G002953", "G003902", "G003579", "G002551", "G004895", "G002001", "G001951", "G001819", "G002797", "G001771", "G001772", "G001554", "G000705", "G000704", "G000701", "G000951", "G001650", "G001651", "G002077", "G003075", "G001006", "G000259", "G004187", "G004565", "G004131", "G004136", "G003208", "G003611", "G005119", "G004762", "G005269", "G005268", "G004768", "G005264", "G005263", "G004299", "G002097", "G000311", "G000316", "G004612", "G005212", "G004349", "G004618", "G001136", "G000101", "G001045", "G001043", "G000005", "G003539", "G003220", "G002755", "G002453", "G005105", "G000030", "G002282"], "ABCDF": [], "BCEF": [], "CDE": [], "CDF": [], "CDEF": ["G004293", "G005246"], "ABE": ["G002821", "G004455", "G003971", "G000024", "G004855"], "ABCD": [], "ABCEF": ["G004239", "G003173", "G004545", "G004051", "G002566", "G002518", "G001525", "G000722", "G001029", "G004391", "G000370", "G003082", "G003602", "G002180", "G005167", "G004789", "G000824", "G005259"], "BDE": [], "ACDE": []}, "name": {"A": "DESeq", "C": "RPKM", "B": "FQ", "E": "TMM", "D": "TC", "F": "UQ"}}], "displaySwitch": "true", "shortNumber": "true", "displayStat": "true"} ;
+$(document).ready(function(){
+  $('#example').jvenn(jvenn_data);
+});
+
+			///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
+			//
+			// Data
+			//
+			///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
+			//var processed_filters = ###PORCESSED_FILTERS### ;
+			/* Example:
+				['filterA', 'filterB', 'filterC']
+			*/
+			//var global_results = ###GLOBAL_RESULTS### ; 
+			/* Example: 
+				{
+					'nb_clstr_kept': 100,
+					'nb_clstr_ini': 300,
+					'nb_seq_kept': 100,
+					'nb_seq_ini': 100000
+				}
+			*/
+			//var by_samples_results = ###SAMPLES_RESULTS### ;
+			/* Example:
+				{
+					'sampleA':{
+						'filtered':{
+							'filterA': 10,
+							'filterB': 20
+						},
+						'initial': 75,
+						'kept': 50
+					},
+					'sampleB':{
+						'filtered':{
+							'filterB': 20,
+						},
+						'initial': 110,
+						'kept': 90
+					}
+				}
+			*/
+			//var by_filters_results = ###FILTERS_RESULTS### ;
+			/* Example:
+				[
+					{'filters':['filterA'], 'count': 10},
+					{'filters':['filterB'], 'count': 20},
+					{'filters':['filterC'], 'count': 30},
+					{'filters':['filterA', 'filterB'], 'count': 1},
+					{'filters':['filterA', 'filterC'], 'count': 2},
+					{'filters':['filterB', 'filterC'], 'count': 3},
+					{'filters':['filterA', 'filterB', 'filterC'], 'count': 4}
+				];
+			*/
+			
+			///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
+			//
+			// Main
+			//
+			///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
+			$(function() {
+				// Remove alert
+				$('#js-alert').remove();
+				$('#content').removeClass("hidden");
+				
+				// Load active tab
+				global_filters_load();
+				intersections_filters_load();
+				
+				// Add tab listener
+				$('.nav-tabs a').click(function (e) {
+					e.preventDefault();
+					$(this).tab('show');
+					if( $(this).attr('href') == "#view-by-samples" && $('#view-by-samples').hasClass('disabled') ){
+						$('#view-by-samples').removeClass('disabled')
+						samples_filters_load( "filter-log" );
+					}
+				})
+			});
+		</script>
+
+	</head>
+	<body>
+		<!-- Alert -->
+		<p id="js-alert" class="alert alert-warning">
+                javascript is needed to display data.<br />
+                If you try to view this data on galaxy please contact your administrator to authorise javascript or download the file to view.
+		</p>
+		
+        <!-- Content -->
+	<div id="example"></div>
+        </div>
+
+		
+	</body>
+</html>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/venn_diagram_text_output.txt	Sun Nov 26 19:09:40 2017 -0500
@@ -0,0 +1,485 @@
+FQ_UQ	FQ_RPKM_TC	DESeq_FQ_RPKM_TMM_UQ	DESeq_FQ_TMM_UQ	FQ	DESeq_TMM_UQ	UQ	FQ_RPKM_TC_TMM_UQ	DESeq_TC_TMM_UQ	DESeq_FQ_TC_TMM_UQ	DESeq	DESeq_FQ	DESeq_TMM	DESeq_FQ_TMM	DESeq_FQ_UQ	DESeq_UQ	FQ_TMM_UQ	TMM_UQ	DESeq_RPKM_TC_TMM_UQ	DESeq_FQ_RPKM_TC_TMM_UQ	RPKM_TC_TMM_UQ	FQ_TC_TMM_UQ	
+G004321	G002462	G004239	G001344	G004580	G001195	G003283	G005214	G001285	G001197	G001905	G002826	G000080	G002821	G000655	G001203	G002976	G001936	G005180	G001598	G004293	G004118	
+G002493		G003173	G004551	G001204	G000114	G002316		G002062	G001193	G000130	G004420	G004384	G004455	G004703	G004708	G000483	G004930		G000305	G005246		
+G001369		G004545	G001597	G002864	G004177	G000950			G001052	G000349	G003424	G002405	G003971	G000046	G003149		G004238		G001343			
+G004173		G004051	G000748	G002803	G001510	G001094			G003936	G002946	G000164	G003427	G000024		G002637		G000875		G000749			
+G002562		G002566	G000620	G003997	G000742	G000919			G003838	G004042	G001536	G004700	G004855		G001114		G001275		G005089			
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+			G002484																			
+			G002957																			
+			G003474																			
+			G002388																			
+			G001083																			
+			G001080																			
+			G002555																			
+			G001394																			
+			G002843																			
+			G001952																			
+			G001073																			
+			G001810																			
+			G001812																			
+			G001776																			
+			G002414																			
+			G002417																			
+			G001227																			
+			G001495																			
+			G001559																			
+			G000468																			
+			G000810																			
+			G000709																			
+			G002671																			
+			G003375																			
+			G004435																			
+			G003076																			
+			G003296																			
+			G000253																			
+			G004220																			
+			G000254																			
+			G001424																			
+			G003949																			
+			G002458																			
+			G000929																			
+			G000927																			
+			G001578																			
+			G004137																			
+			G004501																			
+			G003612																			
+			G004245																			
+			G003201																			
+			G003972																			
+			G004989																			
+			G004988																			
+			G004755																			
+			G004040																			
+			G000405																			
+			G005265																			
+			G004044																			
+			G004980																			
+			G004829																			
+			G002213																			
+			G004290																			
+			G003850																			
+			G004346																			
+			G000317																			
+			G001049																			
+			G003701																			
+			G003538																			
+			G000530																			
+			G000534																			
+			G004535																			
+			G002757																			
+			G002459																			
+			G001910																			
+			G002751																			
+			G002758																			
+			G002320																			
+			G000031																			
+			G001032																			
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/venn_diagram.py	Sun Nov 26 19:09:40 2017 -0500
@@ -0,0 +1,182 @@
+#!/usr/bin/env python2.7
+
+import os
+import sys
+import json
+import operator
+import argparse
+import re
+from itertools import combinations
+
+CURRENT_DIR = os.path.dirname(os.path.abspath(__file__))
+
+##################################################################################################################################################
+# FUNCTIONS
+##################################################################################################################################################
+ 
+def isnumber(format, n):
+    """
+    Check if an element is integer or float
+    """
+    float_format = re.compile("^[\-]?[1-9][0-9]*\.?[0-9]+$")
+    int_format = re.compile("^[\-]?[1-9][0-9]*$")
+    test = ""
+    if format == "int":
+        test = re.match(int_format, n)
+    elif format == "float":
+        test = re.match(float_format, n)
+    if test:
+        return True
+    else:
+        return False
+        
+def input_to_dict(inputs):
+    """
+    Parse input and return a dictionary of name and data of each lists/files
+    """
+    comp_dict = {}
+    title_dict = {}
+    c = ["A", "B", "C", "D", "E", "F"]  
+    for i in range(len(inputs)):
+        input_file = inputs[i][0]        
+        name = inputs[i][1]
+        input_type = inputs[i][2]
+        title = c[i]
+        title_dict[title] = name
+        ids = set()
+        if input_type == "file":
+            header = inputs[i][3]
+            ncol = inputs[i][4]
+            file_content = open(input_file, "r").readlines()
+            
+            # Check if column number is in right form
+            if isnumber("int", ncol.replace("c", "")):
+                if header == "true":
+                    file_content = [x.strip() for x in [line.split("\t")[int(ncol.replace("c", ""))-1].split(";")[0] for line in file_content[1:]]]     # take only first IDs
+                else:
+                    file_content = [x.strip() for x in [line.split("\t")[int(ncol.replace("c", ""))-1].split(";")[0] for line in file_content]]     # take only first IDs
+                #print(file_content[1:13])
+            else:
+                raise ValueError("Please fill in the right format of column number")        
+        else:
+            ids = set()
+            file_content = inputs[i][0].split()
+            
+        ids.update(file_content)
+        comp_dict[title] = ids
+ 
+    return comp_dict, title_dict
+    
+def intersect(comp_dict):
+    """
+    Calculate the intersections of input
+    """
+    names = set(comp_dict)
+    for i in range(1, len(comp_dict) + 1):
+        for group in combinations(sorted(comp_dict), i):
+            others = set()
+            [others.add(name) for name in names if name not in group]
+            difference = []
+            intersected = set.intersection(*(comp_dict[k] for k in group))
+            n = "".join(group)
+            if len(others) > 0:
+                difference = intersected.difference(set.union(*(comp_dict[k] for k in others)))
+            yield group, list(intersected), list(difference)    
+
+def diagram(comp_dict, title_dict):
+    """
+    Create json string for jvenn diagram plot
+    """
+    result = {}
+    result["name"] = {}
+    for k in comp_dict.keys():
+        result["name"][k] = title_dict[k]
+        
+    result["data"] = {}
+    result["values"] = {}    
+    for group, intersected, difference in intersect(comp_dict):
+        if len(group) == 1:
+            result["data"]["".join(group)] = difference
+            result["values"]["".join(group)] = len(difference)
+        elif len(group) > 1 and len(group) < len(comp_dict):
+	        result["data"]["".join(group)] = difference
+	        result["values"]["".join(group)] = len(difference)               
+        elif len(group) == len(comp_dict):
+            result["data"]["".join(group)] = intersected
+            result["values"]["".join(group)] = len(intersected)
+
+    return result
+
+def write_text_venn(json_result):
+    """
+    Write intersections of input to text output file
+    """
+    output = open("venn_diagram_text_output.txt", "w")
+    string = ""
+    lines = []
+    result = dict((k, v) for k, v in json_result["data"].iteritems() if v != [])
+    print(result)
+    max_count = max(len(v) for v in result.values())
+    print(max_count)
+    for i in range(max_count):
+        lines.append("")
+        
+    for i in range(max_count):
+        header = ""
+        for d in range(len(result.keys())):
+            data = result.keys()[d]
+            name = "_".join([json_result["name"][x] for x in data])
+            header += name + "\t"
+            if len(result[data]) > i:
+                lines[i] += result[data][i] + "\t"
+            else:
+                lines[i] += "\t"
+    string += header + "\n"
+    string += "\n".join(lines)
+    print(string)
+    output.write(string)
+    output.close()
+
+def write_summary( summary_file, inputs):
+    """
+    Paste json string into template file
+    """
+    a, b = input_to_dict(inputs)
+    data = diagram(a, b)
+    write_text_venn(data)
+
+    to_replace = {
+    	"series": [data],
+    	"displayStat": "true",
+    	"displaySwitch": "true",
+        "shortNumber": "true",
+    }
+
+    FH_summary_tpl = open(os.path.join(CURRENT_DIR, "jvenn_template.html"))
+    FH_summary_out = open(summary_file, "w" )
+    for line in FH_summary_tpl:
+        if "###JVENN_DATA###" in line:
+            line = line.replace("###JVENN_DATA###", json.dumps(to_replace))
+        FH_summary_out.write(line)
+    
+    FH_summary_out.close()
+    FH_summary_tpl.close()
+   
+def process(args):
+    write_summary(args.summary, args.input)
+
+
+##################################################################################################################################################
+# MAIN
+##################################################################################################################################################
+if __name__ == '__main__':
+    # Parse parameters
+    parser = argparse.ArgumentParser(description='Filters an abundance file')
+    group_input = parser.add_argument_group( 'Inputs' )
+    group_input.add_argument('--input', nargs="+", action="append", required=True, help="The input tabular file.")
+    group_output = parser.add_argument_group( 'Outputs' )
+    group_output.add_argument('--summary', default="summary.html", help="The HTML file containing the graphs. [Default: %(default)s]")
+    args = parser.parse_args()
+
+    # Process
+    process( args )
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/venn_diagram.xml	Sun Nov 26 19:09:40 2017 -0500
@@ -0,0 +1,170 @@
+<?xml version="1.0"?>
+<tool id="Jvenn" name="Venn diagram" version="1.0">
+	<description>compare lists plotting Venn Diagram (based on Jvenn).
+	</description>
+	<command><![CDATA[
+		python $__tool_directory__/venn_diagram.py
+
+		#for $i, $s in enumerate($series)
+		    --input
+		    #if $s.se.input == "file"
+		        "$s.se.file" "$s.se.name" "file" "$s.se.header" "$s.se.ncol"
+		    #else
+                "$s.se.list" "$s.se.name" "list"
+ 		    #end if
+		#end for 
+		--summary "$output_summary"
+	]]></command>
+	<inputs>
+		<!-- Files -->
+		<repeat name="series" title="Lists to compare" min="2" max="6" >
+            <conditional name="se" >
+                    <param type="select" name="input" label="Please provide your identifiers" help="Copy/paste or ID list from a file (e.g. table)" >
+                        <option value="list">Copy/paste your identifiers </option>
+                        <option value="file">Input file containing your identifiers</option>
+                        
+                    </param>
+                    <when value="file">
+                        <param type="data" name="file" format="txt,tabular" label="Choose a file that contains your list of IDs" />
+                        <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does your input file contain header?" />
+		            	<param type="text" name="ncol" value="c1" label="Please specify the column where you would like to apply the comparison" help ='For example, fill in "c1" if you want to filter the first column' />
+		            	<param type="text" name="name" value="" label="Please enter the name of this list" help="This name will be displayed on venn diagram" />
+                    </when>
+                    <when value="list">
+                        <param type="text" name="list" label="Copy/paste your identifiers" help='IDs must be separated by spaces into the form field, for example: P31946 P62258' >
+                            <sanitizer>
+                                <valid initial="string.printable">
+                                    <remove value="&apos;"/>
+                                </valid>
+                                <mapping initial="none">
+                                    <add source="&apos;" target="__sq__"/>
+                                </mapping>
+                            </sanitizer>
+                        </param>
+                        <param type="text" name="name" value="" label="Please enter the name of this list" help="This name will be displayed on venn diagram" />
+                    </when>
+                </conditional>
+		</repeat>
+	</inputs>
+	<outputs>
+		<data format="html" name="output_summary" label="Venn diagram" from_work_dir="venn_diagram_summary.html" />
+		<data format="tabular" name="output_text" label="Venn diagram text output" from_work_dir="venn_diagram_text_output.txt" />
+	</outputs>
+	<tests>
+	    <test>
+	        <repeat name="series">
+	            <conditional name="se">
+	                <param name="input" value="mq_file" />
+	                <param name="mq_file" value="DESeq.txt" />
+	                <param name="header" value="false" />
+	                <param name="ncol" value="c1" />
+	                <param name="name" value="DESeq" />
+	            </conditional>
+	        </repeat>
+	        <repeat name="series">
+	            <conditional name="se">
+	                <param name="input" value="mq_file" />
+	                <param name="mq_file" value="FQ.txt" />
+	                <param name="header" value="false" />
+	                <param name="ncol" value="c1" />
+	                <param name="name" value="FQ" />
+	            </conditional>
+	        </repeat>
+	        <repeat name="series">
+	            <conditional name="se">
+	                <param name="input" value="mq_file" />
+	                <param name="mq_file" value="RPKM.txt" />
+	                <param name="header" value="false" />
+	                <param name="ncol" value="c1" />
+	                <param name="name" value="RPKM" />
+	            </conditional>
+	        </repeat>
+	        <repeat name="series">
+	            <conditional name="se">
+	                <param name="input" value="mq_file" />
+	                <param name="mq_file" value="TC.txt" />
+	                <param name="header" value="false" />
+	                <param name="ncol" value="c1" />
+	                <param name="name" value="TC" />
+	            </conditional>
+	        </repeat>
+	        <repeat name="series">
+	            <conditional name="se">
+	                <param name="input" value="mq_file" />
+	                <param name="mq_file" value="TMM.txt" />
+	                <param name="header" value="false" />
+	                <param name="ncol" value="c1" />
+	                <param name="name" value="TMM" />
+	            </conditional>
+	        </repeat>
+	        <repeat name="series">
+	            <conditional name="se">
+	                <param name="input" value="mq_file" />
+	                <param name="mq_file" value="UQ.txt" />
+	                <param name="header" value="false" />
+	                <param name="ncol" value="c1" />
+	                <param name="name" value="UQ" />
+	            </conditional>
+	        </repeat>
+	        <output name="output_summary" file="venn_diagram_summary.html" />
+	        <output name="output_text" file="venn_diagram_text_output.txt" />
+	                
+	    </test>
+	</tests>
+	<help>
+
+This tool draw a venn diagram from lists/files using Jvenn plug-in (http://jvenn.toulouse.inra.fr/app/index.html). It also creates output files that contain common or specific elements between query and each compared lists/files.
+
+**Inputs**
+
+* **Query file:** A file containing different information of proteins, could be output of previous components.
+
+* **File of a list of IDs:** .TXT format, each line contains 1 ID
+    
+    AMY1A
+    
+ 	ALB
+ 	
+ 	IGKC
+ 	
+ 	CSTA
+ 	
+ 	IGHA1
+ 	
+ 	ACTG1
+
+* **List of IDs:** IDs separated by a space
+    AMY1A ALB IGKC CSTA IGHA1 ACTG1
+
+If you choose a file, it is necessary to specify the column where you would like to perform the comparison.
+
+**Outputs**
+
+* **Summary file** (venn_diagram_summary.html):
+    Venn diagram: Could be downloaded as image (PNG, SVG)
+
+* **Venn text output file**
+    A text file containing common/specific elements among compared lists/files.
+    
+-----
+
+.. class:: infomark
+
+**Authors**
+
+Philippe Bardou, Jérôme Mariette, Frédéric Escudié, Christophe Djemiel and Christophe Klopp. jvenn: an interactive Venn diagram viewer. BMC Bioinformatics 2014, 15:293 doi:10.1186/1471-2105-15-293
+
+.. class:: infomark
+
+**Galaxy integration**
+
+T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR
+
+Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit,Migale Bioinformatics platform
+
+Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool.
+
+	</help> 
+	<citations>
+    </citations>
+</tool>