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changeset 0:57f01ca855cd draft default tip

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"planemo upload commit 47d779aa1de5153673ac8bb1e37c9730210cbb5d"
author galaxyp
date Sat, 12 Jun 2021 18:06:28 +0000
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files README.rst jvenn_template.html releases_notes.rst test-data/Bredberg.txt test-data/ID_Converter_FKW_Lacombe_et_al_2017_OK.txt test-data/Mucilli.txt test-data/Venn_diagram_html.html test-data/Venn_text_output.txt venn_diagram.py venn_diagram.xml
diffstat 10 files changed, 1573 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.rst	Sat Jun 12 18:06:28 2021 +0000
@@ -0,0 +1,49 @@
+Wrapper for JVenn Diagram Tool
+==============================
+
+**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	Sat Jun 12 18:06:28 2021 +0000
@@ -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="https://code.jquery.com/jquery-2.1.3.min.js"></script>
+		<script type="text/javascript" src="https://code.highcharts.com/4.1.4/highcharts.js"></script>
+		<script type="text/javascript" src="https://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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+		</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/releases_notes.rst	Sat Jun 12 18:06:28 2021 +0000
@@ -0,0 +1,19 @@
+=============================
+Venn diagram - Releases Notes
+=============================
+
+==================
+2019-05-13 Release
+==================
+
+New
+---
+
+Improvements
+------------
+
+- handle multiple IDs per line in input file (";" separated)
+- better handle of copy/paste 
+
+Fixes
+-----
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Bredberg.txt	Sat Jun 12 18:06:28 2021 +0000
@@ -0,0 +1,121 @@
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+P11686
+A0A0U1RVJ5
+Q6N093
+Q6MZX7
+Q7Z351
+A0N5G5
+P02787
+Q96P63
+P02768
+P01622
+Q9BYE4
+Q9UBC9
+O95436
+P10599
+P02766
+Q13885
+P25311
+Q96DA0
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ID_Converter_FKW_Lacombe_et_al_2017_OK.txt	Sat Jun 12 18:06:28 2021 +0000
@@ -0,0 +1,152 @@
+Protein accession number (UniProt)	Protein name	Number of peptides (razor + unique)	neXtProt_ID	UniProt.ID	GeneID	MIM	Ensembl
+P15924	Desmoplakin	69	NX_P15924	DESP_HUMAN	1832	125647; 605676; 607450; 607655; 609638; 612908; 615821	ENSG00000096696
+P02538	Keratin, type II cytoskeletal 6A	53	NX_P02538	K2C6A_HUMAN	3853	148041; 615726	ENSG00000205420
+P02768	Serum albumin	44	NX_P02768	ALBU_HUMAN	213	103600; 615999; 616000	ENSG00000163631
+P08779	Keratin, type I cytoskeletal 16	29	NX_P08779	K1C16_HUMAN	3868	148067; 167200; 613000	ENSG00000186832
+Q02413	Desmoglein-1	24	NX_Q02413	DSG1_HUMAN	1828	125670; 148700; 615508	ENSG00000134760
+P07355	Annexin A2;Putative annexin A2-like protein	22	NX_P07355	ANXA2_HUMAN	302	151740	ENSG00000182718
+P14923	Junction plakoglobin	22	NX_P14923	PLAK_HUMAN	3728	173325; 601214; 611528	ENSG00000173801
+P02788	Lactotransferrin	21	NX_P02788	TRFL_HUMAN	4057	150210	ENSG00000012223
+Q9HC84	Mucin-5B	21	NX_Q9HC84	MUC5B_HUMAN	727897	178500; 600770	ENSG00000117983
+P29508	Serpin B3	20	NX_P29508	SPB3_HUMAN	6317	600517	ENSG00000057149
+P63261	Actin, cytoplasmic 2	19	NX_P63261	ACTG_HUMAN	71	102560; 604717; 614583	ENSG00000184009
+Q8N1N4	Keratin, type II cytoskeletal 78	18	NX_Q8N1N4	K2C78_HUMAN	196374	611159	ENSG00000170423
+Q04695	Keratin, type I cytoskeletal 17	18	NX_Q04695	K1C17_HUMAN	3872	148069; 167210; 184500	ENSG00000128422
+P01876	Ig alpha-1 chain C region	16	NX_P01876	IGHA1_HUMAN	NA	146900	ENSG00000211895; ENSG00000282633
+Q01469	Fatty acid-binding protein 5, epidermal	15	NX_Q01469	FABP5_HUMAN	2171	605168	ENSG00000164687
+P31944	Caspase-14	15	NX_P31944	CASPE_HUMAN	23581	605848; 617320	ENSG00000105141
+P01833	Polymeric immunoglobulin receptor	15	NX_P01833	PIGR_HUMAN	5284	173880	ENSG00000162896
+P06733	Alpha-enolase	15	NX_P06733	ENOA_HUMAN	2023	172430	ENSG00000074800
+P25311	Zinc-alpha-2-glycoprotein	15	NX_P25311	ZA2G_HUMAN	563	194460	ENSG00000160862
+Q15149	Plectin	15	NX_Q15149	PLEC_HUMAN	5339	131950; 226670; 601282; 612138; 613723; 616487	ENSG00000178209
+P19013	Keratin, type II cytoskeletal 4	13	NX_P19013	K2C4_HUMAN	NA	123940; 193900	ENSG00000170477
+Q6KB66	Keratin, type II cytoskeletal 80	13	NX_Q6KB66	K2C80_HUMAN	144501	611161	ENSG00000167767
+Q08188	Protein-glutamine gamma-glutamyltransferase E	12	NX_Q08188	TGM3_HUMAN	7053	600238; 617251	ENSG00000125780
+P13646	Keratin, type I cytoskeletal 13	11	NX_P13646	K1C13_HUMAN	3860	148065; 615785	ENSG00000171401
+Q86YZ3	Hornerin	11	NX_Q86YZ3	HORN_HUMAN	388697	616293	ENSG00000197915
+P04259	Keratin, type II cytoskeletal 6B	10	NX_P04259	K2C6B_HUMAN	3854	148042; 615728	ENSG00000185479
+P02545	Prelamin-A/C;Lamin-A/C	10	NX_P02545	LMNA_HUMAN	4000	115200; 150330; 151660; 159001; 176670; 181350; 212112; 248370; 275210; 605588; 610140; 613205; 616516	ENSG00000160789
+P04083	Annexin A1	10	NX_P04083	ANXA1_HUMAN	301	151690	ENSG00000135046
+P11021	78 kDa glucose-regulated protein	10	NX_P11021	GRP78_HUMAN	3309	138120	ENSG00000044574
+P02787	Serotransferrin	9	NX_P02787	TRFE_HUMAN	7018	190000; 209300	ENSG00000091513
+P04040	Catalase	9	NX_P04040	CATA_HUMAN	847	115500; 614097	ENSG00000121691
+P31151	Protein S100-A7	9	NX_P31151	S10A7_HUMAN	6278	600353	ENSG00000143556
+P31947	14-3-3 protein sigma	9	NX_P31947	1433S_HUMAN	2810	601290	ENSG00000175793
+Q96P63	Serpin B12	9	NX_Q96P63	SPB12_HUMAN	89777	615662	ENSG00000166634
+P14618	Pyruvate kinase PKM	9	NX_P14618	KPYM_HUMAN	5315	179050	ENSG00000067225
+P60174	Triosephosphate isomerase	9	NX_P60174	TPIS_HUMAN	7167	190450; 615512	ENSG00000111669
+Q06830	Peroxiredoxin-1	9	NX_Q06830	PRDX1_HUMAN	5052	176763	ENSG00000117450
+P01040	Cystatin-A	8	NX_P01040	CYTA_HUMAN	1475	184600; 607936	ENSG00000121552
+P05089	Arginase-1	8	NX_P05089	ARGI1_HUMAN	383	207800; 608313	ENSG00000118520
+P01834	Ig kappa chain C region	8	NX_P01834	IGKC_HUMAN	NA	147200; 614102	NA
+P04406	Glyceraldehyde-3-phosphate dehydrogenase	8	NX_P04406	G3P_HUMAN	2597	138400	ENSG00000111640
+P0DMV9	Heat shock 70 kDa protein 1B	8	NX_P0DMV9	HS71B_HUMAN	3303; 3304	140550; 603012	ENSG00000204388; ENSG00000224501; ENSG00000212866; ENSG00000231555; ENSG00000232804
+P13639	Elongation factor 2	8	NX_P13639	EF2_HUMAN	1938	130610; 609306	ENSG00000167658
+P35579	Myosin-9	8	NX_P35579	MYH9_HUMAN	4627	153640; 153650; 155100; 160775; 600208; 603622; 605249	ENSG00000100345
+P68371	Tubulin beta-4B chain	8	NX_P68371	TBB4B_HUMAN	10383	602660	ENSG00000188229
+Q8WVV4	Protein POF1B	8	NX_Q8WVV4	POF1B_HUMAN	79983	300603; 300604	ENSG00000124429
+O75635	Serpin B7	7	NX_O75635	SPB7_HUMAN	8710	603357; 615598	ENSG00000166396
+P01857	Ig gamma-1 chain C region	7	NX_P01857	IGHG1_HUMAN	NA	147100; 254500	ENSG00000211896; ENSG00000277633
+P61626	Lysozyme C	7	NX_P61626	LYSC_HUMAN	4069	105200; 153450	ENSG00000090382
+P68363	Tubulin alpha-1B chain	7	NX_P68363	TBA1B_HUMAN	10376	602530	ENSG00000123416
+P01009	Alpha-1-antitrypsin;Short peptide from AAT	6	NX_P01009	A1AT_HUMAN	5265	107400; 613490	ENSG00000197249
+P07900	Heat shock protein HSP 90-alpha	6	NX_P07900	HS90A_HUMAN	3320	140571	ENSG00000080824
+Q9NZH8	Interleukin-36 gamma	6	NX_Q9NZH8	IL36G_HUMAN	56300	605542	ENSG00000136688
+O43707	Alpha-actinin-4;Alpha-actinin-1	6	NX_O43707	ACTN4_HUMAN	81	603278; 604638	ENSG00000130402; ENSG00000282844
+O75223	Gamma-glutamylcyclotransferase	6	NX_O75223	GGCT_HUMAN	79017	137170	ENSG00000006625
+P00338	L-lactate dehydrogenase A chain	6	NX_P00338	LDHA_HUMAN	3939	150000; 612933	ENSG00000134333
+P07339	Cathepsin D	6	NX_P07339	CATD_HUMAN	1509	116840; 610127	ENSG00000117984
+P62987	Ubiquitin-60S ribosomal protein L40	6	NX_P62987	RL40_HUMAN	7311	191321	ENSG00000221983
+P10599	Thioredoxin	6	NX_P10599	THIO_HUMAN	7295	187700	ENSG00000136810
+Q9UGM3	Deleted in malignant brain tumors 1 protein	6	NX_Q9UGM3	DMBT1_HUMAN	1755	137800; 601969	ENSG00000187908
+Q9UI42	Carboxypeptidase A4	6	NX_Q9UI42	CBPA4_HUMAN	51200	607635	ENSG00000128510
+P47929	Galectin-7	5	NX_P47929	LEG7_HUMAN	3963; 653499	600615; 617139	ENSG00000178934; ENSG00000205076; ENSG00000282902; ENSG00000283082
+Q13867	Bleomycin hydrolase	5	NX_Q13867	BLMH_HUMAN	642	602403	ENSG00000108578
+Q6P4A8	Phospholipase B-like 1	5	NX_Q6P4A8	PLBL1_HUMAN	79887	NA	ENSG00000121316
+O75369	Filamin-B	5	NX_O75369	FLNB_HUMAN	2317	108720; 108721; 112310; 150250; 272460; 603381	ENSG00000136068
+P00441	Superoxide dismutase [Cu-Zn]	5	NX_P00441	SODC_HUMAN	6647	105400; 147450	ENSG00000142168
+P04792	Heat shock protein beta-1	5	NX_P04792	HSPB1_HUMAN	3315	602195; 606595; 608634	ENSG00000106211
+P11142	Heat shock cognate 71 kDa protein	5	NX_P11142	HSP7C_HUMAN	3312	600816	ENSG00000109971
+P58107	Epiplakin	5	NX_P58107	EPIPL_HUMAN	83481	607553	NA
+P60842	Eukaryotic initiation factor 4A-I	5	NX_P60842	IF4A1_HUMAN	1973	602641	ENSG00000161960
+P62937	Peptidyl-prolyl cis-trans isomerase A	5	NX_P62937	PPIA_HUMAN	5478	123840	ENSG00000196262
+P63104	14-3-3 protein zeta/delta	5	NX_P63104	1433Z_HUMAN	7534	601288	ENSG00000164924
+Q92820	Gamma-glutamyl hydrolase	5	NX_Q92820	GGH_HUMAN	8836	601509	ENSG00000137563
+O75342	Arachidonate 12-lipoxygenase, 12R-type	4	NX_O75342	LX12B_HUMAN	242	242100; 603741	ENSG00000179477
+P09211	Glutathione S-transferase P	4	NX_P09211	GSTP1_HUMAN	2950	134660	ENSG00000084207
+P31025	Lipocalin-1	4	NX_P31025	LCN1_HUMAN	3933	151675	ENSG00000160349
+P48594	Serpin B4	4	NX_P48594	SPB4_HUMAN	6318	600518	ENSG00000206073
+Q14574	Desmocollin-3	4	NX_Q14574	DSC3_HUMAN	1825	600271; 613102	ENSG00000134762
+Q5T750	Skin-specific protein 32	4	NX_Q5T750	XP32_HUMAN	100129271	NA	ENSG00000198854
+Q6UWP8	Suprabasin	4	NX_Q6UWP8	SBSN_HUMAN	374897	609969	ENSG00000189001
+O60911	Cathepsin L2	4	NX_O60911	CATL2_HUMAN	1515	603308	ENSG00000136943
+P00558	Phosphoglycerate kinase 1	4	NX_P00558	PGK1_HUMAN	5230	300653; 311800	ENSG00000102144
+P04075	Fructose-bisphosphate aldolase A	4	NX_P04075	ALDOA_HUMAN	226	103850; 611881	ENSG00000149925
+P07384	Calpain-1 catalytic subunit	4	NX_P07384	CAN1_HUMAN	823	114220; 616907	ENSG00000014216
+P0CG05	Ig lambda-2 chain C regions	4	NA	NA	NA	NA	NA
+P18206	Vinculin	4	NX_P18206	VINC_HUMAN	7414	193065; 611407; 613255	ENSG00000035403
+P62258	14-3-3 protein epsilon	4	NX_P62258	1433E_HUMAN	7531	605066	ENSG00000108953; ENSG00000274474
+P68871	Hemoglobin subunit beta	4	NX_P68871	HBB_HUMAN	3043	140700; 141900; 603902; 603903; 611162; 613985	ENSG00000244734
+Q9C075	Keratin, type I cytoskeletal 23	4	NX_Q9C075	K1C23_HUMAN	25984	606194	ENSG00000108244; ENSG00000263309
+A8K2U0	Alpha-2-macroglobulin-like protein 1	3	NX_A8K2U0	A2ML1_HUMAN	144568	610627	ENSG00000166535
+P00738	Haptoglobin	3	NX_P00738	HPT_HUMAN	3240	140100; 614081	ENSG00000257017
+P01011	Alpha-1-antichymotrypsin	3	NX_P01011	AACT_HUMAN	12	107280	ENSG00000196136
+P02763	Alpha-1-acid glycoprotein 1	3	NX_P02763	A1AG1_HUMAN	5004	138600	ENSG00000229314
+P18510	Interleukin-1 receptor antagonist protein	3	NX_P18510	IL1RA_HUMAN	3557	147679; 612628; 612852	ENSG00000136689
+P22528	Cornifin-B	3	NX_P22528	SPR1B_HUMAN	6699	182266	ENSG00000169469
+P30740	Leukocyte elastase inhibitor	3	NX_P30740	ILEU_HUMAN	1992	130135	ENSG00000021355
+P80188	Neutrophil gelatinase-associated lipocalin	3	NX_P80188	NGAL_HUMAN	3934	600181	ENSG00000148346
+Q15828	Cystatin-M	3	NX_Q15828	CYTM_HUMAN	1474	601891	ENSG00000175315
+Q9HCY8	Protein S100-A14	3	NX_Q9HCY8	S10AE_HUMAN	57402	607986	ENSG00000189334
+P01623	Ig kappa chain V-III region	3	NA	NA	NA	NA	NA
+P01877	Ig alpha-2 chain C region	3	NX_P01877	IGHA2_HUMAN	NA	147000	ENSG00000211890
+P06396	Gelsolin	3	NX_P06396	GELS_HUMAN	2934	105120; 137350	ENSG00000148180
+P14735	Insulin-degrading enzyme	3	NX_P14735	IDE_HUMAN	3416	146680	ENSG00000119912
+P20933	N(4)-(beta-N-acetylglucosaminyl)-L-asparaginase	3	NX_P20933	ASPG_HUMAN	175	208400; 613228	ENSG00000038002
+P25788	Proteasome subunit alpha type-3	3	NX_P25788	PSA3_HUMAN	5684	176843; 176845	ENSG00000100567
+P26641	Elongation factor 1-gamma	3	NX_P26641	EF1G_HUMAN	1937	130593	ENSG00000254772
+P36952	Serpin B5	3	NX_P36952	SPB5_HUMAN	5268	154790	ENSG00000206075
+P40926	Malate dehydrogenase, mitochondrial	3	NX_P40926	MDHM_HUMAN	4191	154100; 617339	ENSG00000146701
+Q9Y6R7	IgGFc-binding protein	3	NX_Q9Y6R7	FCGBP_HUMAN	8857	617553	ENSG00000281123
+O95274	Ly6/PLAUR domain-containing protein 3	2	NX_O95274	LYPD3_HUMAN	27076	609484	ENSG00000124466
+P00491	Purine nucleoside phosphorylase	2	NX_P00491	PNPH_HUMAN	4860	164050; 613179	ENSG00000198805
+P04080	Cystatin-B	2	NX_P04080	CYTB_HUMAN	1476	254800; 601145	ENSG00000160213
+P09972	Fructose-bisphosphate aldolase C	2	NX_P09972	ALDOC_HUMAN	230	103870	ENSG00000109107
+P19012	Keratin, type I cytoskeletal 15	2	NX_P19012	K1C15_HUMAN	3866	148030	ENSG00000171346
+P20930	Filaggrin	2	NX_P20930	FILA_HUMAN	2312	135940; 146700; 605803	ENSG00000143631
+Q96FX8	p53 apoptosis effector related to PMP-22	2	NX_Q96FX8	PERP_HUMAN	64065	609301	ENSG00000112378
+Q9UIV8	Serpin B13	2	NX_Q9UIV8	SPB13_HUMAN	5275	604445	ENSG00000197641
+P01625	Ig kappa chain V-IV region Len	2	NA	NA	NA	NA	NA
+P01765	Ig heavy chain V-III region TIL	2	NA	NA	NA	NA	NA
+P01766	Ig heavy chain V-III region BRO	2	NX_P01766	HV313_HUMAN	NA	NA	ENSG00000211942; ENSG00000282286
+P01860	Ig gamma-3 chain C region	2	NX_P01860	IGHG3_HUMAN	NA	147120	NA
+P01871	Ig mu chain C region	2	NX_P01871	IGHM_HUMAN	NA	147020; 601495	ENSG00000211899; ENSG00000282657
+P05090	Apolipoprotein D	2	NX_P05090	APOD_HUMAN	347	107740	ENSG00000189058
+P06870	Kallikrein-1	2	NX_P06870	KLK1_HUMAN	3816	147910; 615953	ENSG00000167748
+P07858	Cathepsin B	2	NX_P07858	CATB_HUMAN	1508	116810	ENSG00000164733
+P08865	40S ribosomal protein SA	2	NX_P08865	RSSA_HUMAN	3921	150370; 271400	ENSG00000168028
+P11279	Lysosome-associated membrane glycoprotein 1	2	NX_P11279	LAMP1_HUMAN	3916	153330	ENSG00000185896
+P13473	Lysosome-associated membrane glycoprotein 2	2	NX_P13473	LAMP2_HUMAN	3920	300257; 309060	ENSG00000005893
+P19971	Thymidine phosphorylase	2	NX_P19971	TYPH_HUMAN	1890	131222; 603041	ENSG00000025708
+P23284	Peptidyl-prolyl cis-trans isomerase B	2	NX_P23284	PPIB_HUMAN	5479	123841; 259440	ENSG00000166794
+P23396	40S ribosomal protein S3	2	NX_P23396	RS3_HUMAN	6188	600454	ENSG00000149273
+P25705	ATP synthase subunit alpha, mitochondrial	2	NX_P25705	ATPA_HUMAN	498	164360; 615228; 616045	ENSG00000152234
+P27482	Calmodulin-like protein 3	2	NX_P27482	CALL3_HUMAN	810	114184	ENSG00000178363
+P31949	Protein S100-A11	2	NX_P31949	S10AB_HUMAN	6282	603114	ENSG00000163191
+P40121	Macrophage-capping protein	2	NX_P40121	CAPG_HUMAN	822	153615	ENSG00000042493
+P42357	Histidine ammonia-lyase	2	NX_P42357	HUTH_HUMAN	3034	235800; 609457	ENSG00000084110
+P47756	F-actin-capping protein subunit beta	2	NX_P47756	CAPZB_HUMAN	832	601572	ENSG00000077549
+P48637	Glutathione synthetase	2	NX_P48637	GSHB_HUMAN	2937	231900; 266130; 601002	ENSG00000100983
+P49720	Proteasome subunit beta type-3	2	NX_P49720	PSB3_HUMAN	5691	602176	ENSG00000277791; ENSG00000275903
+P50395	Rab GDP dissociation inhibitor beta	2	NX_P50395	GDIB_HUMAN	2665	600767	ENSG00000057608
+P59998	Actin-related protein 2/3 complex subunit 4	2	NX_P59998	ARPC4_HUMAN	10093	604226	ENSG00000241553
+P61160	Actin-related protein 2	2	NX_P61160	ARP2_HUMAN	10097	604221	ENSG00000138071
+P61916	Epididymal secretory protein E1	2	NX_P61916	NPC2_HUMAN	10577	601015; 607625	ENSG00000119655
+P04745	Alpha-amylase 1	23	NX_P04745	AMY1_HUMAN	276; 277; 278	104700; 104701; 104702	ENSG00000174876; ENSG00000187733; ENSG00000237763
+Q9NZT1	Calmodulin-like protein 5	8	NX_Q9NZT1	CALL5_HUMAN	51806	605183	ENSG00000178372
+P12273	Prolactin-inducible protein	6	NX_P12273	PIP_HUMAN	5304	176720	ENSG00000159763
+Q96DA0	Zymogen granule protein 16 homolog B	5	NX_Q96DA0	ZG16B_HUMAN	124220	NA	ENSG00000162078; ENSG00000283056
+P01036	Cystatin-S	5	NX_P01036	CYTS_HUMAN	1472	123857	ENSG00000101441
+Q8TAX7	Mucin-7	2	NX_Q8TAX7	MUC7_HUMAN	4589	158375; 600807	ENSG00000171195
+P01037	Cystatin-SN	2	NX_P01037	CYTN_HUMAN	1469	123855	ENSG00000170373
+P09228	Cystatin-SA	2	NX_P09228	CYTT_HUMAN	1470	123856	ENSG00000170369
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Mucilli.txt	Sat Jun 12 18:06:28 2021 +0000
@@ -0,0 +1,167 @@
+P04264
+P35908
+P35527
+P04259
+P13647
+P08779
+P02533
+Q04695
+P01040
+P13645
+P59665
+Q01469
+Q9NZT1
+P22531
+P04792
+P01834
+Q96KK5
+Q06830
+P60709
+P13646
+P31949
+P06702
+P14923
+Q13835
+P60174
+P07737
+P62805
+P31947
+P10599
+P15924
+Q6UWP8
+P02768
+Q6KB66
+P12035
+P47929
+P04406
+P17931
+Q3ZCW2
+P63167
+P63104
+P0CG48
+Q5XKE5
+P11142
+P06733
+Q7Z794
+P01593
+Q9NZH8
+P14174
+P01620
+P36952
+P68104
+O60814
+Q8N1N4
+P00338
+Q02413
+P07355
+P52907
+Q6ZVX7
+P08865
+P09211
+Q96P63
+P68371
+P30041
+P27482
+P08107
+P22392
+P29508
+P01861
+Q08188
+Q9C075
+P14618
+P31025
+P02679
+P54652
+Q13748
+P01857
+P80188
+P35321
+P02675
+P19013
+Q14CN4
+P37802
+P05783
+P51149
+P01876
+P28072
+Q86YZ3
+Q5T749
+P28070
+P05109
+P02671
+P58107
+Q5T750
+P04040
+P00558
+P62244
+P03973
+Q6E0U4
+P47756
+P13639
+P68431
+P32119
+Q8WVV4
+Q96QA5
+P68871
+Q9Y337
+P11021
+P01871
+P61626
+P25311
+P22735
+P30050
+P06576
+O43175
+O43790
+P37837
+P04083
+P04075
+P02545
+P50990
+O43707
+Q5D862
+P17900
+O75223
+Q14134
+Q08554
+P60842
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Venn_diagram_html.html	Sat Jun 12 18:06:28 2021 +0000
@@ -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="https://code.jquery.com/jquery-2.1.3.min.js"></script>
+		<script type="text/javascript" src="https://code.highcharts.com/4.1.4/highcharts.js"></script>
+		<script type="text/javascript" src="https://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">
+/*
+$(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 = {"series": [{"name": {"A": "Lacombe", "B": "Bredberg", "C": "Mucilli"}, "data": {"A": ["A8K2U0", "O60911", "O75342", "O75635", "O95274", "P00441", "P00491", "P01037", "P01623", "P01766", "P01860", "P01877", "P02538", "P04080", "P04745", "P06870", "P07384", "P07858", "P09228", "P09972", "P0CG05", "P0DMV9", "P11279", "P13473", "P18510", "P19012", "P19971", "P20930", "P23284", "P23396", "P25705", "P25788", "P30740", "P31151", "P35579", "P40121", "P42357", "P48594", "P48637", "P49720", "P50395", "P59998", "P61160", "P62258", "P62937", "P62987", "P63261", "P68363", "Q14574", "Q15149", "Q15828", "Q6P4A8", "Q8TAX7", "Q92820", "Q96FX8", "Q9HC84", "Q9HCY8", "Q9UI42", "Q9Y6R7", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", ""], "B": ["A0A0U1RVJ5", "A0N5G5", "A2IPI6", "A4F255", "B4E1Z4", "O95436", "O95613", "P00450", "P00734", "P01008", "P01024", "P01591", "P01598", "P01611", "P01613", "P01617", "P01621", "P01622", "P01714", "P01717", "P01880", "P02647", "P02649", "P02747", "P02751", "P02760", "P02766", "P02774", "P02790", "P04117", "P04196", "P04217", "P04233", "P04637", "P05155", "P05362", "P06313", "P06681", "P08238", "P08758", "P0C0L4", "P0C0L5", "P10909", "P11217", "P11686", "P12429", "P15814", "P19827", "P22897", "P23528", "P43652", "P61769", "P62807", "P80748", "Q08380", "Q13885", "Q14624", "Q16378", "Q6MZX7", "Q6N093", "Q7Z351", "Q86SJ6", "Q8IWL2", "Q8NF17", "Q96S96", "Q9BYE4", "Q9NSK0", "Q9UBC9", "Q9UL77", "Q9UL83", "Q9UL86", "", "", "", "", "", "", "", "", ""], "C": ["O15523", "O43175", "O43790", "O60814", "P01593", "P01620", "P01861", "P02533", "P02671", "P02675", "P02679", "P03973", "P04264", "P05091", "P05120", "P05783", "P06576", "P06702", "P07476", "P08107", "P0CG48", "P10809", "P12035", "P13489", "P13645", "P13647", "P14174", "P15880", "P17900", "P17931", "P22392", "P22531", "P22735", "P23490", "P23526", "P25787", "P28070", "P28072", "P28074", "P29373", "P29401", "P30041", "P30050", "P32119", "P35321", "P35527", "P35908", "P37802", "P37837", "P40925", "P49189", "P49862", "P50990", "P51149", "P52907", "P54652", "P61978", "P62244", "P63167", "P68104", "P68431", "Q08554", "Q13748", "Q14134", "Q14210", "Q14CN4", "Q15365", "Q3ZCW2", "Q5T749", "Q5VVQ6", "Q5XKE5", "Q6E0U4", "Q6ZVX7", "Q7Z794", "Q8IW75", "Q96KK5", "Q96QA5", "Q9Y277", "Q9Y337", "Q9Y3R4"], "AB": ["P01009", "P01011", "P01036", "P01625", "P01765", "P01833", "P02763", "P02787", "P12273", "P22528", "P61916", "Q13867", "Q96DA0", "Q9UGM3", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", ""], "AC": ["O43707", "O75223", "O75369", "P00558", "P01040", "P01834", "P01857", "P01876", "P02545", "P04040", "P04075", "P04259", "P04792", "P05090", "P06733", "P08779", "P08865", "P09211", "P11021", "P11142", "P13639", "P13646", "P14618", "P14735", "P14923", "P18206", "P19013", "P20933", "P26641", "P29508", "P31944", "P31949", "P36952", "P40926", "P47756", "P47929", "P58107", "P60174", "P60842", "P68371", "Q04695", "Q06830", "Q5T750", "Q6KB66", "Q6UWP8", "Q8N1N4", "Q8WVV4", "Q9C075", "Q9NZH8", "Q9NZT1", "Q9UIV8", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", ""], "BC": ["P01023", "P05109", "P07737", "P59665", "P60709", "P62805", "Q13835", "Q15517", "Q5D862", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", ""], "ABC": ["P00338", "P00738", "P01871", "P02768", "P02788", "P04083", "P04406", "P05089", "P06396", "P07339", "P07355", "P07900", "P10599", "P15924", "P25311", "P27482", "P31025", "P31947", "P61626", "P63104", "P68871", "P80188", "Q01469", "Q02413", "Q08188", "Q86YZ3", "Q96P63", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", ""]}, "values": {"A": 59, "B": 71, "C": 80, "AB": 14, "AC": 51, "BC": 9, "ABC": 27}}], "displayStat": "true", "displaySwitch": "true", "shortNumber": "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_text_output.txt	Sat Jun 12 18:06:28 2021 +0000
@@ -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="https://code.jquery.com/jquery-2.1.3.min.js"></script>
+		<script type="text/javascript" src="https://code.highcharts.com/4.1.4/highcharts.js"></script>
+		<script type="text/javascript" src="https://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">
+/*
+$(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 = {"series": [{"name": {"A": "Lacombe", "B": "Bredberg", "C": "Mucilli"}, "data": {"A": ["Q15828", "P59998", "Q9HCY8", "P40121", "Q14574", "P06870", "P09972", "P48637", "Q96FX8", "O75635", "Q6P4A8", "P50395", "P19971", "P63261", "P04745", "P0CG05", "Q9UI42", "P42357", "P23396", "P25788", "O60911", "P0DMV9", "P18510", "P01623", "P68363", "Q15149", "P01860", "P30740", "P20930", "A8K2U0", "Q9HC84", "P07858", "P04080", "P35579", "P00491", "Q9Y6R7", "P01877", "P25705", "P00441", "P62937", "Q8TAX7", "P09228", "Q92820", "P61160", "P49720", "P02538", "P19012", "P23284", "P48594", "O95274", "P07384", "P13473", "P31151", "P01766", "P62258", "P62987", "O75342", "P11279", "P01037", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", ""], "B": ["P01611", "P02774", "P01008", "P01598", "Q16378", "Q9NSK0", "P02649", "A4F255", "P04196", "Q96S96", "P22897", "P01024", "P02647", "P0C0L4", "O95436", "P80748", "P08238", "Q86SJ6", "P04233", "P06681", "P04637", "Q9UL83", "P11686", "P10909", "Q7Z351", "P23528", "Q14624", "P01880", "Q13885", "Q8IWL2", "Q8NF17", "P04217", "O95613", "P11217", "P05155", "P01621", "A2IPI6", "Q08380", "P0C0L5", "P19827", "P02747", "Q6N093", "A0A0U1RVJ5", "P01717", "B4E1Z4", "P02760", "Q9UL77", "P15814", "P00450", "Q9UL86", "P01613", "P01617", "Q9BYE4", "P08758", "P02766", "A0N5G5", "P02790", "P04117", "P61769", "P43652", "Q6MZX7", "P01714", "P00734", "P05362", "P01591", "P62807", "P12429", "P02751", "P06313", "Q9UBC9", "P01622", "", "", "", "", "", "", "", "", ""], "C": ["P68431", "P51149", "P13647", "Q3ZCW2", "P01593", "P07476", "P32119", "Q14CN4", "P01861", "P01620", "P23490", "P0CG48", "P12035", "P54652", "P10809", "Q96KK5", "P37802", "O15523", "P17931", "Q5T749", "Q6E0U4", "P06576", "P13489", "P23526", "P28070", "P28074", "P35527", "Q14134", "P30050", "P05120", "P52907", "P68104", "Q08554", "P29401", "P15880", "P49862", "P22392", "P40925", "P62244", "Q7Z794", "P22531", "Q14210", "P03973", "Q8IW75", "P08107", "O60814", "P35321", "P14174", "Q5XKE5", "P02671", "P28072", "P02675", "P29373", "O43790", "P05091", "Q5VVQ6", "Q9Y277", "O43175", "P17900", "P63167", "P49189", "Q6ZVX7", "P02679", "P04264", "Q9Y337", "P30041", "Q96QA5", "P22735", "P06702", "P25787", "Q9Y3R4", "P37837", "P02533", "P05783", "P50990", "P35908", "P61978", "Q15365", "P13645", "Q13748"], "AB": ["P02763", "P01009", "P12273", "P01833", "P02787", "Q13867", "P01036", "P61916", "P01625", "P22528", "P01765", "Q96DA0", "P01011", "Q9UGM3", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", ""], "AC": ["P31949", "O75223", "P60842", "P14923", "P18206", "Q9NZT1", "P09211", "Q9UIV8", "P01857", "P04040", "O75369", "Q8WVV4", "P47756", "P40926", "P05090", "P60174", "Q9C075", "P20933", "P04792", "P29508", "P11142", "P01040", "Q5T750", "P14618", "P13639", "P04075", "P31944", "P14735", "Q04695", "P58107", "P19013", "P36952", "P01876", "P08779", "P08865", "P11021", "P00558", "P06733", "Q6UWP8", "Q6KB66", "P04259", "P68371", "Q9NZH8", "P26641", "P13646", "P02545", "Q8N1N4", "Q06830", "P01834", "O43707", "P47929", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", ""], "BC": ["P07737", "P60709", "Q5D862", "Q15517", "Q13835", "P05109", "P62805", "P01023", "P59665", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", ""], "ABC": ["Q96P63", "P80188", "P10599", "P01871", "P31025", "Q86YZ3", "P27482", "P02768", "P07355", "P63104", "P04406", "P15924", "Q08188", "P07339", "P05089", "Q01469", "P31947", "P68871", "P61626", "P06396", "P00338", "P00738", "Q02413", "P07900", "P02788", "P25311", "P04083", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", ""]}, "values": {"A": 59, "B": 71, "C": 80, "AB": 14, "AC": 51, "BC": 9, "ABC": 27}}], "displayStat": "true", "displaySwitch": "true", "shortNumber": "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') ){
+						$('#view-by-samples').removeClass('disabled')
+						samples_filters_load( "filter-log" );
+					}
+				})
+			});
+		</script>
+
+	</head>
+	<body>
+		<!-- Alert -->
+		<p id="js-alert" class="alert alert-warning">
+                javascript is needed to display data.<br />
+                If you try to view this data on galaxy please contact your administrator to authorise javascript or download the file to view.
+		</p>
+		
+        <!-- Content -->
+	<div id="example"></div>
+        </div>
+
+		
+	</body>
+</html>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/venn_diagram.py	Sat Jun 12 18:06:28 2021 +0000
@@ -0,0 +1,204 @@
+#!/usr/bin/env python
+
+import argparse
+import csv
+import json
+import os
+import re
+from itertools import combinations
+
+
+CURRENT_DIR = os.path.dirname(os.path.abspath(__file__))
+
+########################################################################
+# FUNCTIONS
+########################################################################
+
+
+def isnumber(format, n):
+    """
+    Check if an element is integer or float
+    """
+    float_format = re.compile(r"^[-]?[1-9][0-9]*.?[0-9]+$")
+    int_format = re.compile(r"^[-]?[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]
+            with open(input_file, "r") as handle:
+                file_content = csv.reader(handle, delimiter="\t")
+                file_content = list(file_content)   # csv object to list
+
+                # Check if column number is in right form
+                if isnumber("int", ncol.replace("c", "")):
+                    if header == "true":
+                        # gets ids from defined column
+                        file_content = [x for x in [line[int(ncol.replace("c", ""))-1].split(";") for line in file_content[1:]]]  # noqa 501
+
+                    else:
+                        file_content = [x for x in [line[int(ncol.replace("c", ""))-1].split(";") for line in file_content]]  # noqa 501
+                else:
+                    raise ValueError("Please fill in the right format of column number")  # noqa 501
+        else:
+            ids = set()
+            file_content = inputs[i][0].split()
+            file_content = [x.split(";") for x in file_content]
+
+        # flat list of list of lists, remove empty items
+        file_content = [item.strip() for sublist in file_content for item in sublist if item != '']   # noqa 501
+        ids.update(file_content)
+        if 'NA' in ids:
+            ids.remove('NA')
+        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))
+            if len(others) > 0:
+                difference = intersected.difference(set.union(*(comp_dict[k] for k in others))) # noqa 501
+            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)] = sorted(difference)
+            result["values"]["".join(group)] = len(difference)
+        elif len(group) > 1 and len(group) < len(comp_dict):
+            result["data"]["".join(group)] = sorted(difference)
+            result["values"]["".join(group)] = len(difference)
+        elif len(group) == len(comp_dict):
+            result["data"]["".join(group)] = sorted(intersected)
+            result["values"]["".join(group)] = len(intersected)
+
+    return result
+
+# Write intersections of input to text output file
+
+
+def write_text_venn(json_result):
+    lines = []
+    result = dict((k, v) for k, v in json_result["data"].items() if v != [])  # noqa 501
+    for key in result:
+        if 'NA' in result[key]:
+            result[key].remove("NA")
+
+    list_names = dict((k, v) for k, v in json_result["name"].items() if v != [])  # noqa 501
+    nb_lines_max = max(len(v) for v in result.values())
+
+    # get list names associated to each column
+    column_dict = {}
+    for key in result:
+        if key in list_names:
+            column_dict[key] = list_names[key]
+        else:
+            keys = list(key)
+            column_dict[key] = "_".join([list_names[k] for k in keys])
+
+    # construct tsv
+    for key in result:
+        line = result[key]
+        if len(line) < nb_lines_max:
+            line.extend([''] * (nb_lines_max - len(line)))
+        line = [column_dict[key]] + line     # add header
+        lines.append(line)
+    # transpose tsv
+    lines = zip(*lines)
+
+    with open("venn_diagram_text_output.tsv", "w") as output:
+        tsv_output = csv.writer(output, delimiter='\t')
+        tsv_output.writerows(lines)
+
+
+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	Sat Jun 12 18:06:28 2021 +0000
@@ -0,0 +1,177 @@
+<?xml version="1.0"?>
+<tool id="proteore_venn_diagram" name="Venn diagram" version="2021.06.08" profile="20.01">
+    <description>with JVenn</description>
+    <requirements>
+        <requirement type="package" version="3.9">python</requirement>
+    </requirements>
+    <command detect_errors="aggressive"><![CDATA[
+        python '$__tool_directory__/venn_diagram.py'
+
+        #for $i, $s in enumerate($series)
+            --input
+            #if $s.se.input == "file"
+                '$s.se.file' '$s.name' 'file' '$s.se.header' '$s.se.ncol'
+            #else
+                '$s.se.list' '$s.name' 'list'
+             #end if
+        #end for 
+        --summary '$output_summary'
+    ]]></command>
+    <inputs>
+        <repeat name="series" title="List to compare" min="2" max="6">
+            <conditional name="se" >
+                <param type="select" name="input" label="Enter your list" help="Copy/paste or from a file (e.g. table)" >
+                    <option value="list">Copy/paste list </option>
+                    <option value="file" selected="true">Input file containing your list</option>
+                </param>
+                <when value="file">
+                    <param type="data" name="file" format="txt,tabular" label="Select your file" />
+                    <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does file contain header?" />
+                    <param type="text" name="ncol" value="c1" label="Column number on which apply the comparison" help ='For example, fill in "c1" if you want to filter the first column'>
+                        <validator type="regex" message="Please enter a column number, for example: 'c1' for the first column">[c]{0,1}[0-9]+</validator>
+                    </param>
+                </when>
+                <when value="list">
+                    <param type="text" name="list" label="Copy/paste list" help='IDs must be separated by spaces into the form field, for example: P31946 P62258' >
+                        <sanitizer>
+                            <valid initial="string.printable">
+                                <remove value="&apos;"/>
+                                <remove value="/"/>
+                            </valid>
+                            <mapping initial="none">
+                                <add source="&apos;" target="__sq__"/>
+                            </mapping>
+                        </sanitizer>
+                    </param>
+                </when>
+            </conditional>
+            <param type="text" name="name" value="" label="Enter the name of this list" help="This name will be displayed on venn diagram" optional="false">
+                <sanitizer>
+                    <valid initial="string.printable">
+                        <remove value="&apos;"/>
+                    </valid>
+                    <mapping initial="none">
+                        <add source="&apos;" target="__sq__"/>
+                    </mapping>
+                </sanitizer>
+                <validator type="regex" message="Please enter a list name">[a-zA-Z0-9._-]+</validator>
+            </param>
+        </repeat>
+    </inputs>
+    <outputs>
+        <data format="html" name="output_summary" label="Venn diagram" from_work_dir="venn_diagram_summary.html" />
+        <data format="tsv" name="output_text" label="Venn diagram text output" from_work_dir="venn_diagram_text_output.tsv" />
+    </outputs>
+    <tests>
+        <test>
+            <repeat name="series">
+                <conditional name="se">
+                    <param name="input" value="file" />
+                    <param name="file" value="ID_Converter_FKW_Lacombe_et_al_2017_OK.txt" />
+                    <param name="header" value="true" />
+                    <param name="ncol" value="c1" />
+                </conditional>
+                 <param name="name" value="Lacombe" />
+            </repeat>
+            <repeat name="series">
+                <conditional name="se">
+                    <param name="input" value="file" />
+                    <param name="file" value="Bredberg.txt" />
+                    <param name="header" value="false" />
+                    <param name="ncol" value="c1" />
+                </conditional>
+                <param name="name" value="Bredberg" />
+            </repeat>
+            <repeat name="series">
+                <conditional name="se">
+                    <param name="input" value="file" />
+                    <param name="file" value="Mucilli.txt" />
+                    <param name="header" value="false" />
+                    <param name="ncol" value="c1" />
+                </conditional>
+                <param name="name" value="Mucilli" />
+            </repeat>
+            <output name="output_summary" file="Venn_diagram_html.html" />
+            <!-- <output name="output_text" file="Venn_text_output.txt" />       -->
+        </test>
+    </tests>
+    <help><![CDATA[
+
+**Description**
+
+This tool is used for cross-comparison purpose between several lists having a common key (e.g. IDs) and draw a venn diagram from lists/files using the Jvenn plug-in (see Authors below).
+It also creates output text file that contain common or specific elements between query and each compared lists/files.
+
+-----
+
+**Input**
+
+Can be either a list entered in a copy/paste mode or a single or multi-columns file (txt, tsv, csv, tab, output from other tools) up to six lists/files
+
+* **List of IDs in a copy/paste mode:** IDs have to be separated by a space (e.g. AMY1A ALB IGKC CSTA IGHA1 ACTG1)
+        
+* **for example an IDs list file** in .txt format, with 1 ID per line
+
+.. csv-table:: tab1
+    :header: "Ids"
+
+
+    "AMY1A"
+    "ALB"    
+    "IGKC"    
+    "CSTA"    
+    "IGHA1"
+        
+If you use a file as input list, it is necessary to specify the column number on which to apply the comparison.
+
+Ids in a line will be split by ";", so if you have this kind of input : 
+
+.. csv-table:: tab with multiple ids per line
+    :header: "Ids"
+
+    "P22531"
+    "P04792"
+    "P01834"
+    "Q96KK5"
+    "Q06830;P60709;P13646;P31949"
+    "P06702"
+    "P14923"
+    "Q13835"
+
+All ID will be considered (i.e. Q06830,P60709,P13646 and P31949 will be split).
+
+.. class:: warningmark
+    
+In copy/paste mode, the number of IDs considered in input is limited to 5000.
+
+-----
+
+**Parameter**
+
+"Please enter the name of this list": each list or set should be named, this information will be reported in both output (see below)
+
+-----
+
+**Output**
+
+Two outputs are generated:
+        
+* **Graphical file**: Venn diagram that you can either display (interactive mode) or download as an image (PNG, SVG format)
+        
+* **Venn text output file** : a text file containing specific elements or shared by lists/files.
+
+
+]]></help>
+   <citations>
+         <citation type="doi">doi:10.1186/1471-2105-15-293</citation>
+         <citation type="bibtex">@book{toolsProteoRE,
+            journal = {GitHub repository},
+            publisher = {GitHub},
+            title = {ProteoRE tools},
+            url = {https://github.com/galaxyproteomics/tools-galaxyp},
+            author = {Lien Nguyen, David Chistiany, Florence Combes,Christophe Caron, Valentin Loux Yves Vandenbrouck},
+            date = {2021},
+            year = {2021},
+        }</citation>
+   </citations>
+</tool>