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Changeset 0:9d4f20618ab4 (2017-11-26)

Next changeset 1:760470ddb9ca (2018-02-16)

Commit message:
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty

added:
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

diff -r 000000000000 -r 9d4f20618ab4 README.rst
--- /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.

diff -r 000000000000 -r 9d4f20618ab4 jvenn_template.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/jvenn_template.html Sun Nov 26 19:09:40 2017 -0500

[

b'@@ -0,0 +1,228 @@\n+<!DOCTYPE html>\n+\n+<html>\n+\t<head>\n+\t\t<title>Jvenn+</title>\n+\t\t<meta charset="UTF-8">\n+\t\t<meta name="version" content="2.0.1">\n+\t\t<link rel="stylesheet" href="https://cdn.datatables.net/1.10.6/css/jquery.dataTables.css"></link>\n+\t\t<link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.4/css/bootstrap.min.css"></link>\n+\t\t<style type="text/css">\n+\t\t\t#js-alert {\n+\t\t\t\twidth: 90%;\n+\t\t\t\tmargin-right: auto;\n+\t\t\t\tmargin-left: auto;\n+\t\t\t}\n+\t\t\t#content {\n+\t\t\t\twidth: 90%;\n+\t\t\t\tmargin-right: auto;\n+\t\t\t\tmargin-left: auto;\n+\t\t\t}\n+\t\t\t.clear {\n+\t\t\t\tclear: both;\n+\t\t\t\theight: 0px;\n+\t\t\t\twidth: 100%;\n+\t\t\t\tfloat: none !important;\n+\t\t\t}\n+\t\t\tul.nav-tabs {\n+\t\t\t\tmargin-bottom: 30px;\n+\t\t\t}\n+\t\t\t#venn-filters {\n+\t\t\t\tpadding: 10px;\n+\t\t\t\tbackground-color: #FFF;\n+\t\t\t\tbackground-clip: padding-box;\n+\t\t\t\tborder: 1px solid rgba(0, 0, 0, 0.15);\n+\t\t\t\tborder-radius: 4px;\n+\t\t\t\tbox-shadow: 0px 6px 12px rgba(0, 0, 0, 0.176);\n+\t\t\t\tmargin-right: auto;\n+\t\t\t\tmargin-left: auto;\n+\t\t\t\tmargin-bottom: 30px;\n+\t\t\t}\n+\t\t\t#byFilters-jvenn {\n+\t\t\t\tmargin-right: auto;\n+\t\t\t\tmargin-left: auto;\n+\t\t\t}\n+\t\t\t#venn-filters ul {\n+\t\t\t\tlist-style-type: none;\n+\t\t\t}\n+\t\t</style>\n+\n+\t\t<script type="text/javascript" src="http://code.jquery.com/jquery-2.1.3.min.js"></script>\n+\t\t<script type="text/javascript" src="http://code.highcharts.com/4.1.4/highcharts.js"></script>\n+\t\t<script type="text/javascript" src="http://code.highcharts.com/4.1.4/modules/exporting.js"></script>\n+\t\t<script type="text/javascript" src="https://cdn.datatables.net/1.10.6/js/jquery.dataTables.min.js"></script>\n+\t\t<script type="text/javascript" src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.4/js/bootstrap.min.js"></script>\n+\t\t<script type="text/javascript">\n+\t\t\t/***************************************************************\n+\t\t\t* Copyright notice\n+\t\t\t*\n+\t\t\t* (c) 2014 PF bioinformatique de Toulouse\n+\t\t\t* All rights reserved\n+\t\t\t* \n+\t\t\t*\n+\t\t\t* This script is an adaptation of the venny script developed by\n+\t\t\t* Juan Carlos Oliveros, BioinfoGP, CNB-CSIC:\n+\t\t\t* Oliveros, J.C. (2007) VENNY. An interactive tool for comparing \n+\t\t\t* lists with Venn Diagrams.\n+\t\t\t* http://bioinfogp.cnb.csic.es/tools/venny/index.html.\n+\t\t\t* It is distributed under the terms of the GNU General Public \n+\t\t\t* License as published by the Free Software Foundation; either \n+\t\t\t* version 2 of the License, or (at your option) any later version.\n+\t\t\t*\n+\t\t\t* The GNU General Public License can be found at\n+\t\t\t* http://www.gnu.org/copyleft/gpl.html.\n+\t\t\t*\n+\t\t\t* This script is distributed in the hope that it will be useful,\n+\t\t\t* but WITHOUT ANY WARRANTY; without even the implied warranty of\n+\t\t\t* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\n+\t\t\t* GNU General Public License for more details.\n+\t\t\t*\n+\t\t\t* This copyright notice MUST APPEAR in all copies of the script!\n+\t\t\t***************************************************************/\n+\t\t\t!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)];'..b'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);\n+\t\t</script>\t\t\n+\t\t\n+\t\t<script type="text/javascript">\n+/*\n+$(document).ready(function(){\n+ $(\'#example\').jvenn({\n+ series: [{\n+ \tname: {A: \'Actors\',\n+ B: \'Singers\'},\n+ \tdata: {A: ["Arnold Schwarzenegger", "Jack Nicholson", "Robert de Niro", "Harrison Ford"], B: ["Freddy Mercury", "Ricky Martin", "Celine Dion"], AB: ["Marilyn Monroe", "Barbra Streisand", "Dean Martin"]},\n+ \tvalues: {A: 4, B: 3, AB: 3}\n+ }],\n+ });\n+});\n+*/\n+var jvenn_data = ###JVENN_DATA### ;\n+$(document).ready(function(){\n+ $(\'#example\').jvenn(jvenn_data);\n+});\n+\n+\t\t\t///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////\n+\t\t\t//\n+\t\t\t// Data\n+\t\t\t//\n+\t\t\t///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////\n+\t\t\t//var processed_filters = ###PORCESSED_FILTERS### ;\n+\t\t\t/* Example:\n+\t\t\t\t[\'filterA\', \'filterB\', \'filterC\']\n+\t\t\t*/\n+\t\t\t//var global_results = ###GLOBAL_RESULTS### ; \n+\t\t\t/* Example: \n+\t\t\t\t{\n+\t\t\t\t\t\'nb_clstr_kept\': 100,\n+\t\t\t\t\t\'nb_clstr_ini\': 300,\n+\t\t\t\t\t\'nb_seq_kept\': 100,\n+\t\t\t\t\t\'nb_seq_ini\': 100000\n+\t\t\t\t}\n+\t\t\t*/\n+\t\t\t//var by_samples_results =\xc2\xa0###SAMPLES_RESULTS### ;\n+\t\t\t/* Example:\n+\t\t\t\t{\n+\t\t\t\t\t\'sampleA\':{\n+\t\t\t\t\t\t\'filtered\':{\n+\t\t\t\t\t\t\t\'filterA\': 10,\n+\t\t\t\t\t\t\t\'filterB\': 20\n+\t\t\t\t\t\t},\n+\t\t\t\t\t\t\'initial\': 75,\n+\t\t\t\t\t\t\'kept\': 50\n+\t\t\t\t\t},\n+\t\t\t\t\t\'sampleB\':{\n+\t\t\t\t\t\t\'filtered\':{\n+\t\t\t\t\t\t\t\'filterB\': 20,\n+\t\t\t\t\t\t},\n+\t\t\t\t\t\t\'initial\': 110,\n+\t\t\t\t\t\t\'kept\': 90\n+\t\t\t\t\t}\n+\t\t\t\t}\n+\t\t\t*/\n+\t\t\t//var by_filters_results =\xc2\xa0###FILTERS_RESULTS### ;\n+\t\t\t/* Example:\n+\t\t\t\t[\n+\t\t\t\t\t{\'filters\':[\'filterA\'], \'count\': 10},\n+\t\t\t\t\t{\'filters\':[\'filterB\'], \'count\': 20},\n+\t\t\t\t\t{\'filters\':[\'filterC\'], \'count\': 30},\n+\t\t\t\t\t{\'filters\':[\'filterA\', \'filterB\'], \'count\': 1},\n+\t\t\t\t\t{\'filters\':[\'filterA\', \'filterC\'], \'count\': 2},\n+\t\t\t\t\t{\'filters\':[\'filterB\', \'filterC\'], \'count\': 3},\n+\t\t\t\t\t{\'filters\':[\'filterA\', \'filterB\', \'filterC\'], \'count\': 4}\n+\t\t\t\t];\n+\t\t\t*/\n+\t\t\t\n+\t\t\t///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////\n+\t\t\t//\n+\t\t\t// Main\n+\t\t\t//\n+\t\t\t///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////\n+\t\t\t$(function() {\n+\t\t\t\t// Remove alert\n+\t\t\t\t$(\'#js-alert\').remove();\n+\t\t\t\t$(\'#content\').removeClass("hidden");\n+\t\t\t\t\n+\t\t\t\t// Load active tab\n+\t\t\t\tglobal_filters_load();\n+\t\t\t\tintersections_filters_load();\n+\t\t\t\t\n+\t\t\t\t// Add tab listener\n+\t\t\t\t$(\'.nav-tabs a\').click(function (e) {\n+\t\t\t\t\te.preventDefault();\n+\t\t\t\t\t$(this).tab(\'show\');\n+\t\t\t\t\tif( $(this).attr(\'href\') == "#view-by-samples" && $(\'#view-by-samples\').hasClass(\'disabled\') ){\n+\t\t\t\t\t\t$(\'#view-by-samples\').removeClass(\'disabled\')\n+\t\t\t\t\t\tsamples_filters_load( "filter-log" );\n+\t\t\t\t\t}\n+\t\t\t\t})\n+\t\t\t});\n+\t\t</script>\n+\n+\t</head>\n+\t<body>\n+\t\t\n+\t\t<p id="js-alert" class="alert alert-warning">\n+ javascript is needed to display data.<br />\n+ If you try to view this data on galaxy please contact your administrator to authorise javascript or download the file to view.\n+\t\t</p>\n+\t\t\n+ \n+\t<div id="example"></div>\n+ </div>\n+\n+\t\t\n+\t</body>\n+</html>\n'

diff -r 000000000000 -r 9d4f20618ab4 test-data/DESeq.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/DESeq.txt Sun Nov 26 19:09:40 2017 -0500

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diff -r 000000000000 -r 9d4f20618ab4 test-data/FQ.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/FQ.txt Sun Nov 26 19:09:40 2017 -0500

b'@@ -0,0 +1,1092 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366\n+G003368\n+G003375\n+G003381\n+G003388\n+G003390\n+G003403\n+G003411\n+G003424\n+G003446\n+G003464\n+G003474\n+G003480\n+G003486\n+G003500\n+G003502\n+G003503\n+G003511\n+G003522\n+G003538\n+G003539\n+G003542\n+G003543\n+G003544\n+G003550\n+G003558\n+G003570\n+G003576\n+G003579\n+G003588\n+G003589\n+G003592\n+G003593\n+G003594\n+G003596\n+G003601\n+G003602\n+G003611\n+G003612\n+G003619\n+G003625\n+G003628\n+G003634\n+G003637\n+G003643\n+G003645\n+G003648\n+G003649\n+G003661\n+G003670\n+G003678\n+G003688\n+G003695\n+G003699\n+G003701\n+G003709\n+G003729\n+G003733\n+G003746\n+G003747\n+G003758\n+G003760\n+G003766\n+G003770\n+G003776\n+G003784\n+G003791\n+G003794\n+G003800\n+G003808\n+G003818\n+G003823\n+G003828\n+G003836\n+G003838\n+G003843\n+G003847\n+G003850\n+G003865\n+G003881\n+G003892\n+G003898\n+G003901\n+G003902\n+G003903\n+G003905\n+G003906\n+G003912\n+G003915\n+G003919\n+G003928\n+G003931\n+G003936\n+G003938\n+G003948\n+G003949\n+G003953\n+G003956\n+G003962\n+G003964\n+G003971\n+G003972\n+G003980\n+G003997\n+G004004\n+G004007\n+G004009\n+G004011\n+G004014\n+G004021\n+G004022\n+G004034\n+G004037\n+G004040\n+G004044\n+G004051\n+G004059\n+G004061\n+G004064\n+G004082\n+G004086\n+G004088\n+G004095\n+G004096\n+G004099\n+G004104\n+G004108\n+G004113\n+G004115\n+G004118\n+G004119\n+G004120\n+G004121\n+G004123\n+G004131\n+G004136\n+G004137\n+G004144\n+G004151\n+G004160\n+G004161\n+G004170\n+G004173\n+G004187\n+G004191\n+G004192\n+G004203\n+G004206\n+G004210\n+G004213\n+G004220\n+G004237\n+G004239\n+G004241\n+G004243\n+G004245\n+G004258\n+G004260\n+G004262\n+G004273\n+G004276\n+G004290\n+G004299\n+G004302\n+G004307\n+G004321\n+G004324\n+G004325\n+G004328\n+G004329\n+G004330\n+G004331\n+G004332\n+G004334\n+G004346\n+G004349\n+G004350\n+G004351\n+G004353\n+G004365\n+G004373\n+G004377\n+G004389\n+G004391\n+G004392\n+G004394\n+G004398\n+G004404\n+G004410\n+G004411\n+G004420\n+G004421\n+G004424\n+G004428\n+G004431\n+G004435\n+G004438\n+G004439\n+G004445\n+G004455\n+G004458\n+G004462\n+G004466\n+G004467\n+G004468\n+G004469\n+G004470\n+G004471\n+G004473\n+G004475\n+G004477\n+G004478\n+G004479\n+G004481\n+G004484\n+G004485\n+G004487\n+G004491\n+G004492\n+G004501\n+G004520\n+G004532\n+G004535\n+G004537\n+G004539\n+G004543\n+G004545\n+G004547\n+G004551\n+G004554\n+G004556\n+G004558\n+G004565\n+G004568\n+G004577\n+G004578\n+G004580\n+G004589\n+G004593\n+G004604\n+G004610\n+G004612\n+G004618\n+G004623\n+G004625\n+G004635\n+G004643\n+G004648\n+G004649\n+G004657\n+G004671\n+G004679\n+G004693\n+G004695\n+G004697\n+G004698\n+G004699\n+G004703\n+G004704\n+G004712\n+G004713\n+G004714\n+G004715\n+G004718\n+G004729\n+G004730\n+G004733\n+G004735\n+G004740\n+G004743\n+G004745\n+G004749\n+G004753\n+G004755\n+G004762\n+G004768\n+G004772\n+G004783\n+G004784\n+G004789\n+G004793\n+G004795\n+G004814\n+G004829\n+G004832\n+G004850\n+G004855\n+G004856\n+G004860\n+G004863\n+G004867\n+G004874\n+G004883\n+G004885\n+G004887\n+G004892\n+G004895\n+G004907\n+G004922\n+G004925\n+G004932\n+G004934\n+G004944\n+G004947\n+G004967\n+G004972\n+G004980\n+G004982\n+G004988\n+G004989\n+G004992\n+G004999\n+G005001\n+G005002\n+G005014\n+G005019\n+G005021\n+G005023\n+G005024\n+G005031\n+G005033\n+G005043\n+G005044\n+G005050\n+G005053\n+G005055\n+G005073\n+G005089\n+G005091\n+G005094\n+G005095\n+G005105\n+G005114\n+G005118\n+G005119\n+G005121\n+G005126\n+G005131\n+G005138\n+G005142\n+G005148\n+G005149\n+G005154\n+G005159\n+G005167\n+G005169\n+G005172\n+G005173\n+G005175\n+G005176\n+G005178\n+G005182\n+G005184\n+G005185\n+G005188\n+G005192\n+G005196\n+G005198\n+G005199\n+G005200\n+G005201\n+G005202\n+G005203\n+G005204\n+G005212\n+G005214\n+G005220\n+G005222\n+G005227\n+G005231\n+G005234\n+G005237\n+G005241\n+G005243\n+G005248\n+G005250\n+G005254\n+G005255\n+G005259\n+G005263\n+G005264\n+G005265\n+G005266\n+G005268\n+G005269\n+G005273\n+G005274\n+G005276\n'

diff -r 000000000000 -r 9d4f20618ab4 test-data/RPKM.txt
--- /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 @@
+G000005
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diff -r 000000000000 -r 9d4f20618ab4 test-data/TC.txt
--- /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 @@
+G000005
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+G000026
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+G000029
+G000030
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diff -r 000000000000 -r 9d4f20618ab4 test-data/TMM.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/TMM.txt Sun Nov 26 19:09:40 2017 -0500

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diff -r 000000000000 -r 9d4f20618ab4 test-data/UQ.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/UQ.txt Sun Nov 26 19:09:40 2017 -0500

b'@@ -0,0 +1,1213 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diff -r 000000000000 -r 9d4f20618ab4 test-data/venn_diagram_summary.html
--- /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

[

b'@@ -0,0 +1,228 @@\n+<!DOCTYPE html>\n+\n+<html>\n+\t<head>\n+\t\t<title>Jvenn+</title>\n+\t\t<meta charset="UTF-8">\n+\t\t<meta name="version" content="2.0.1">\n+\t\t<link rel="stylesheet" href="https://cdn.datatables.net/1.10.6/css/jquery.dataTables.css"></link>\n+\t\t<link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.4/css/bootstrap.min.css"></link>\n+\t\t<style type="text/css">\n+\t\t\t#js-alert {\n+\t\t\t\twidth: 90%;\n+\t\t\t\tmargin-right: auto;\n+\t\t\t\tmargin-left: auto;\n+\t\t\t}\n+\t\t\t#content {\n+\t\t\t\twidth: 90%;\n+\t\t\t\tmargin-right: auto;\n+\t\t\t\tmargin-left: auto;\n+\t\t\t}\n+\t\t\t.clear {\n+\t\t\t\tclear: both;\n+\t\t\t\theight: 0px;\n+\t\t\t\twidth: 100%;\n+\t\t\t\tfloat: none !important;\n+\t\t\t}\n+\t\t\tul.nav-tabs {\n+\t\t\t\tmargin-bottom: 30px;\n+\t\t\t}\n+\t\t\t#venn-filters {\n+\t\t\t\tpadding: 10px;\n+\t\t\t\tbackground-color: #FFF;\n+\t\t\t\tbackground-clip: padding-box;\n+\t\t\t\tborder: 1px solid rgba(0, 0, 0, 0.15);\n+\t\t\t\tborder-radius: 4px;\n+\t\t\t\tbox-shadow: 0px 6px 12px rgba(0, 0, 0, 0.176);\n+\t\t\t\tmargin-right: auto;\n+\t\t\t\tmargin-left: auto;\n+\t\t\t\tmargin-bottom: 30px;\n+\t\t\t}\n+\t\t\t#byFilters-jvenn {\n+\t\t\t\tmargin-right: auto;\n+\t\t\t\tmargin-left: auto;\n+\t\t\t}\n+\t\t\t#venn-filters ul {\n+\t\t\t\tlist-style-type: none;\n+\t\t\t}\n+\t\t</style>\n+\n+\t\t<script type="text/javascript" src="http://code.jquery.com/jquery-2.1.3.min.js"></script>\n+\t\t<script type="text/javascript" src="http://code.highcharts.com/4.1.4/highcharts.js"></script>\n+\t\t<script type="text/javascript" src="http://code.highcharts.com/4.1.4/modules/exporting.js"></script>\n+\t\t<script type="text/javascript" src="https://cdn.datatables.net/1.10.6/js/jquery.dataTables.min.js"></script>\n+\t\t<script type="text/javascript" src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.4/js/bootstrap.min.js"></script>\n+\t\t<script type="text/javascript">\n+\t\t\t/***************************************************************\n+\t\t\t* Copyright notice\n+\t\t\t*\n+\t\t\t* (c) 2014 PF bioinformatique de Toulouse\n+\t\t\t* All rights reserved\n+\t\t\t* \n+\t\t\t*\n+\t\t\t* This script is an adaptation of the venny script developed by\n+\t\t\t* Juan Carlos Oliveros, BioinfoGP, CNB-CSIC:\n+\t\t\t* Oliveros, J.C. (2007) VENNY. An interactive tool for comparing \n+\t\t\t* lists with Venn Diagrams.\n+\t\t\t* http://bioinfogp.cnb.csic.es/tools/venny/index.html.\n+\t\t\t* It is distributed under the terms of the GNU General Public \n+\t\t\t* License as published by the Free Software Foundation; either \n+\t\t\t* version 2 of the License, or (at your option) any later version.\n+\t\t\t*\n+\t\t\t* The GNU General Public License can be found at\n+\t\t\t* http://www.gnu.org/copyleft/gpl.html.\n+\t\t\t*\n+\t\t\t* This script is distributed in the hope that it will be useful,\n+\t\t\t* but WITHOUT ANY WARRANTY; without even the implied warranty of\n+\t\t\t* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\n+\t\t\t* GNU General Public License for more details.\n+\t\t\t*\n+\t\t\t* This copyright notice MUST APPEAR in all copies of the script!\n+\t\t\t***************************************************************/\n+\t\t\t!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)];'..b'"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"} ;\n+$(document).ready(function(){\n+ $(\'#example\').jvenn(jvenn_data);\n+});\n+\n+\t\t\t///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////\n+\t\t\t//\n+\t\t\t// Data\n+\t\t\t//\n+\t\t\t///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////\n+\t\t\t//var processed_filters = ###PORCESSED_FILTERS### ;\n+\t\t\t/* Example:\n+\t\t\t\t[\'filterA\', \'filterB\', \'filterC\']\n+\t\t\t*/\n+\t\t\t//var global_results = ###GLOBAL_RESULTS### ; \n+\t\t\t/* Example: \n+\t\t\t\t{\n+\t\t\t\t\t\'nb_clstr_kept\': 100,\n+\t\t\t\t\t\'nb_clstr_ini\': 300,\n+\t\t\t\t\t\'nb_seq_kept\': 100,\n+\t\t\t\t\t\'nb_seq_ini\': 100000\n+\t\t\t\t}\n+\t\t\t*/\n+\t\t\t//var by_samples_results =\xc2\xa0###SAMPLES_RESULTS### ;\n+\t\t\t/* Example:\n+\t\t\t\t{\n+\t\t\t\t\t\'sampleA\':{\n+\t\t\t\t\t\t\'filtered\':{\n+\t\t\t\t\t\t\t\'filterA\': 10,\n+\t\t\t\t\t\t\t\'filterB\': 20\n+\t\t\t\t\t\t},\n+\t\t\t\t\t\t\'initial\': 75,\n+\t\t\t\t\t\t\'kept\': 50\n+\t\t\t\t\t},\n+\t\t\t\t\t\'sampleB\':{\n+\t\t\t\t\t\t\'filtered\':{\n+\t\t\t\t\t\t\t\'filterB\': 20,\n+\t\t\t\t\t\t},\n+\t\t\t\t\t\t\'initial\': 110,\n+\t\t\t\t\t\t\'kept\': 90\n+\t\t\t\t\t}\n+\t\t\t\t}\n+\t\t\t*/\n+\t\t\t//var by_filters_results =\xc2\xa0###FILTERS_RESULTS### ;\n+\t\t\t/* Example:\n+\t\t\t\t[\n+\t\t\t\t\t{\'filters\':[\'filterA\'], \'count\': 10},\n+\t\t\t\t\t{\'filters\':[\'filterB\'], \'count\': 20},\n+\t\t\t\t\t{\'filters\':[\'filterC\'], \'count\': 30},\n+\t\t\t\t\t{\'filters\':[\'filterA\', \'filterB\'], \'count\': 1},\n+\t\t\t\t\t{\'filters\':[\'filterA\', \'filterC\'], \'count\': 2},\n+\t\t\t\t\t{\'filters\':[\'filterB\', \'filterC\'], \'count\': 3},\n+\t\t\t\t\t{\'filters\':[\'filterA\', \'filterB\', \'filterC\'], \'count\': 4}\n+\t\t\t\t];\n+\t\t\t*/\n+\t\t\t\n+\t\t\t///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////\n+\t\t\t//\n+\t\t\t// Main\n+\t\t\t//\n+\t\t\t///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////\n+\t\t\t$(function() {\n+\t\t\t\t// Remove alert\n+\t\t\t\t$(\'#js-alert\').remove();\n+\t\t\t\t$(\'#content\').removeClass("hidden");\n+\t\t\t\t\n+\t\t\t\t// Load active tab\n+\t\t\t\tglobal_filters_load();\n+\t\t\t\tintersections_filters_load();\n+\t\t\t\t\n+\t\t\t\t// Add tab listener\n+\t\t\t\t$(\'.nav-tabs a\').click(function (e) {\n+\t\t\t\t\te.preventDefault();\n+\t\t\t\t\t$(this).tab(\'show\');\n+\t\t\t\t\tif( $(this).attr(\'href\') == "#view-by-samples" && $(\'#view-by-samples\').hasClass(\'disabled\') ){\n+\t\t\t\t\t\t$(\'#view-by-samples\').removeClass(\'disabled\')\n+\t\t\t\t\t\tsamples_filters_load( "filter-log" );\n+\t\t\t\t\t}\n+\t\t\t\t})\n+\t\t\t});\n+\t\t</script>\n+\n+\t</head>\n+\t<body>\n+\t\t\n+\t\t<p id="js-alert" class="alert alert-warning">\n+ javascript is needed to display data.<br />\n+ If you try to view this data on galaxy please contact your administrator to authorise javascript or download the file to view.\n+\t\t</p>\n+\t\t\n+ \n+\t<div id="example"></div>\n+ </div>\n+\n+\t\t\n+\t</body>\n+</html>\n'

diff -r 000000000000 -r 9d4f20618ab4 test-data/venn_diagram_text_output.txt
--- /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

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No newline at end of file\n'

diff -r 000000000000 -r 9d4f20618ab4 venn_diagram.py
--- /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 )

diff -r 000000000000 -r 9d4f20618ab4 venn_diagram.xml
--- /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>
+ 
+ <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="'"/>
+                                </valid>
+                                <mapping initial="none">
+                                    <add source="'" 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>