changeset 11:958eb2ea02aa draft default tip

"planemo upload commit 00cab92333b0338cb86ff78b5bbc1b6d26621012-dirty"
author proteore
date Wed, 12 May 2021 16:48:05 +0000
parents e744a43171ff
children
files test-data/Venn_diagram_html.html test-data/Venn_text_output.txt venn_diagram.py venn_diagram.xml
diffstat 4 files changed, 333 insertions(+), 166 deletions(-) [+]
line wrap: on
line diff
--- a/test-data/Venn_diagram_html.html	Tue Jan 14 09:14:27 2020 -0500
+++ b/test-data/Venn_diagram_html.html	Wed May 12 16:48:05 2021 +0000
@@ -62,9 +62,9 @@
 			}
 		</style>
 
-		<script type="text/javascript" src="http://code.jquery.com/jquery-2.1.3.min.js"></script>
-		<script type="text/javascript" src="http://code.highcharts.com/4.1.4/highcharts.js"></script>
-		<script type="text/javascript" src="http://code.highcharts.com/4.1.4/modules/exporting.js"></script>
+		<script type="text/javascript" src="https://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">
@@ -95,8 +95,8 @@
 			*  This copyright notice MUST APPEAR in all copies of the script!
 			***************************************************************/
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class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC000010"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC110000"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC101000"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC100100"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC100010"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC011000"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC010100"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC010010"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" 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t=!1;s("*[id^=item]").each(function(){"on"===s(this).children("span").text()&&(t=!0)});var e=!1;if(null!=B.searchInput&&""!=B.searchInput.val()&&(e=!0),!t&&!e&&""!==s(this).text()){var l=this.listnames,r=this;s("*[id^=label]").each(function(){l.indexOf(s(this).text())<0?s(this).css("opacity",.1):s(this).css("opacity",.6)}),s(".number-black").each(function(){this!=r&&s(this).css("opacity",.1)}),b(),"edwards"==B.displayMode?y(c[1]):x(c[1]),B.displayStat&&v(c[1])}},function(){var t=!1;s("*[id^=item]").each(function(){"on"===s(this).children("span").text()&&(t=!0)});var e=!1;if(null!=B.searchInput&&""!=B.searchInput.val()&&(e=!0),!t&&!e&&""!==s(this).text()){{this.listnames}s("*[id^=label]").each(function(){s(this).css("opacity",.5)}),s(".number-black").each(function(){s(this).css("opacity",1)}),b(),"edwards"==B.displayMode?y(c[1]):x(c[1]),B.displayStat&&v(c[1])}}),s("#canvasEllipse").html(j.getSvg())}),this}}(jQuery);
 		</script>
 		<script type="text/javascript">
 			/*
@@ -129,7 +129,7 @@
   });
 });
 */
-var jvenn_data = {"series": [{"values": {"A": 59, "C": 71, "B": 80, "BC": 9, "AC": 14, "ABC": 27, "AB": 51}, "data": {"A": ["P0DMV9", "Q9Y6R7", "P30740", "P68363", "O75635", "O60911", "P61160", "Q15828", "P23284", "P20930", "P01860", "Q96FX8", "P62937", "Q15149", "P25705", "P19971", "O75342", "Q92820", "P25788", "Q9HCY8", "P19012", "Q8TAX7", "P42357", "P50395", "P01766", "P40121", "P04080", "Q9HC84", "P59998", "P23396", "P00491", "P62258", "P01623", "P31151", "Q6P4A8", "P63261", "P01877", "P09228", "P48637", "P07858", "P07384", "P06870", "Q9UI42", "P35579", "P13473", "P62987", "P04745", "P49720", "P11279", "P18510", "Q14574", "P02538", "P48594", "A8K2U0", "P09972", "O95274", "P01037", "P0CG05", "P00441"], "C": ["P04217", "P02649", "Q7Z351", "P08758", "Q9UBC9", "P02760", "O95436", "P02647", "P15814", "Q9NSK0", "P01717", "P04117", "Q13885", "P01591", "O95613", "P01880", "P04233", "P01598", "P01621", "Q9UL77", "P05362", "P01024", "Q86SJ6", "P12429", "P43652", "P22897", "P06313", "B4E1Z4", "P01008", "A2IPI6", "P02790", "P61769", "P00450", "Q08380", "P02751", "Q8NF17", "Q14624", "P0C0L5", "P0C0L4", "Q9UL83", "P08238", "P02766", "Q9UL86", "P02774", "P05155", "P11686", "P01622", "Q6N093", "P04637", "Q96S96", "P62807", "P23528", "P10909", "A4F255", "P00734", "P19827", "Q16378", "P01714", "P11217", "A0A0U1RVJ5", "P01617", "P01611", "P04196", "P01613", "P02747", "P80748", "A0N5G5", "Q8IWL2", "Q9BYE4", "P06681", "Q6MZX7"], "B": ["Q7Z794", "P51149", "P17900", "Q96KK5", "P10809", "O43175", "Q6ZVX7", "P01861", "P14174", "P01593", "Q15365", "P37802", "P29373", "P30050", "Q6E0U4", "P23526", "Q13748", "P05120", "Q14134", "P68431", "P35527", "Q5XKE5", "O15523", "P25787", "P22392", "P49189", "P61978", "P32119", "Q5VVQ6", "Q8IW75", "P01620", "P02671", "P62244", "P0CG48", "P02675", "Q9Y277", "P02679", "P02533", "Q9Y337", "P12035", "P52907", "P35321", "P13489", "P29401", "P04264", "Q14210", "P28074", "P40925", "P28070", "P28072", "Q14CN4", "Q9Y3R4", "P13647", "P54652", "Q08554", "P08107", "P30041", "P06702", "O43790", "Q96QA5", "P23490", "P22735", "P13645", "P17931", "Q3ZCW2", "P68104", "P06576", "Q5T749", "P05091", "O60814", "P37837", "P22531", "P03973", "P63167", "P05783", "P50990", "P15880", "P35908", "P07476", "P49862"], "BC": ["Q13835", "P01023", "P59665", "Q15517", "P05109", "P60709", "P62805", "Q5D862", "P07737"], "AC": ["P02787", "P01833", "P01625", "P22528", "Q9UGM3", "Q96DA0", "P02763", "P61916", "P01009", "P12273", "Q13867", "P01765", "P01036", "P01011"], "ABC": ["P02768", "P10599", "P07355", "Q01469", "P68871", "P07900", "P15924", "P25311", "Q86YZ3", "P05089", "Q08188", "P04406", "P07339", "P06396", "P00338", "P61626", "P04083", "Q02413", "P27482", "P01871", "P80188", "P31947", "P31025", "Q96P63", "P63104", "P00738", "P02788"], "AB": ["P08779", "P04259", "O75223", "P47756", "P06733", "P20933", "Q9NZH8", "P09211", "P04792", "P36952", "P01040", "P60174", "P26641", "P14618", "P31944", "Q8N1N4", "P04075", "P14923", "Q8WVV4", "O75369", "P00558", "P19013", "Q5T750", "P14735", "P47929", "Q06830", "P29508", "P68371", "Q9NZT1", "P11142", "P40926", "P01876", "P58107", "P01834", "P18206", "Q04695", "P08865", "P13646", "P02545", "P04040", "P13639", "P05090", "Q6KB66", "P01857", "Q6UWP8", "Q9UIV8", "Q9C075", "O43707", "P11021", "P31949", "P60842"]}, "name": {"A": "Lacombe", "C": "Bredberg", "B": "Mucilli"}}], "displaySwitch": "true", "shortNumber": "true", "displayStat": "true"} ;
+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);
 });
@@ -152,7 +152,7 @@
 					'nb_seq_ini': 100000
 				}
 			*/
-			//var by_samples_results = ###SAMPLES_RESULTS### ;
+			//var by_samples_results = ###SAMPLES_RESULTS### ;
 			/* Example:
 				{
 					'sampleA':{
@@ -172,7 +172,7 @@
 					}
 				}
 			*/
-			//var by_filters_results = ###FILTERS_RESULTS### ;
+			//var by_filters_results = ###FILTERS_RESULTS### ;
 			/* Example:
 				[
 					{'filters':['filterA'], 'count': 10},
--- a/test-data/Venn_text_output.txt	Tue Jan 14 09:14:27 2020 -0500
+++ b/test-data/Venn_text_output.txt	Wed May 12 16:48:05 2021 +0000
@@ -1,81 +1,228 @@
-Lacombe	Bredberg	Mucilli	Mucilli_Bredberg	Lacombe_Bredberg	Lacombe_Mucilli_Bredberg	Lacombe_Mucilli	
-P0DMV9	P04217	Q7Z794	Q13835	P02787	P02768	P08779	
-Q9Y6R7	P02649	P51149	P01023	P01833	P10599	P04259	
-P30740	Q7Z351	P17900	P59665	P01625	P07355	O75223	
-P68363	P08758	Q96KK5	Q15517	P22528	Q01469	P47756	
-O75635	Q9UBC9	P10809	P05109	Q9UGM3	P68871	P06733	
-O60911	P02760	O43175	P60709	Q96DA0	P07900	P20933	
-P61160	O95436	Q6ZVX7	P62805	P02763	P15924	Q9NZH8	
-Q15828	P02647	P01861	Q5D862	P61916	P25311	P09211	
-P23284	P15814	P14174	P07737	P01009	Q86YZ3	P04792	
-P20930	Q9NSK0	P01593		P12273	P05089	P36952	
-P01860	P01717	Q15365		Q13867	Q08188	P01040	
-Q96FX8	P04117	P37802		P01765	P04406	P60174	
-P62937	Q13885	P29373		P01036	P07339	P26641	
-Q15149	P01591	P30050		P01011	P06396	P14618	
-P25705	O95613	Q6E0U4			P00338	P31944	
-P19971	P01880	P23526			P61626	Q8N1N4	
-O75342	P04233	Q13748			P04083	P04075	
-Q92820	P01598	P05120			Q02413	P14923	
-P25788	P01621	Q14134			P27482	Q8WVV4	
-Q9HCY8	Q9UL77	P68431			P01871	O75369	
-P19012	P05362	P35527			P80188	P00558	
-Q8TAX7	P01024	Q5XKE5			P31947	P19013	
-P42357	Q86SJ6	O15523			P31025	Q5T750	
-P50395	P12429	P25787			Q96P63	P14735	
-P01766	P43652	P22392			P63104	P47929	
-P40121	P22897	P49189			P00738	Q06830	
-P04080	P06313	P61978			P02788	P29508	
-Q9HC84	B4E1Z4	P32119				P68371	
-P59998	P01008	Q5VVQ6				Q9NZT1	
-P23396	A2IPI6	Q8IW75				P11142	
-P00491	P02790	P01620				P40926	
-P62258	P61769	P02671				P01876	
-P01623	P00450	P62244				P58107	
-P31151	Q08380	P0CG48				P01834	
-Q6P4A8	P02751	P02675				P18206	
-P63261	Q8NF17	Q9Y277				Q04695	
-P01877	Q14624	P02679				P08865	
-P09228	P0C0L5	P02533				P13646	
-P48637	P0C0L4	Q9Y337				P02545	
-P07858	Q9UL83	P12035				P04040	
-P07384	P08238	P52907				P13639	
-P06870	P02766	P35321				P05090	
-Q9UI42	Q9UL86	P13489				Q6KB66	
-P35579	P02774	P29401				P01857	
-P13473	P05155	P04264				Q6UWP8	
-P62987	P11686	Q14210				Q9UIV8	
-P04745	P01622	P28074				Q9C075	
-P49720	Q6N093	P40925				O43707	
-P11279	P04637	P28070				P11021	
-P18510	Q96S96	P28072				P31949	
-Q14574	P62807	Q14CN4				P60842	
-P02538	P23528	Q9Y3R4					
-P48594	P10909	P13647					
-A8K2U0	A4F255	P54652					
-P09972	P00734	Q08554					
-O95274	P19827	P08107					
-P01037	Q16378	P30041					
-P0CG05	P01714	P06702					
-P00441	P11217	O43790					
-	A0A0U1RVJ5	Q96QA5					
-	P01617	P23490					
-	P01611	P22735					
-	P04196	P13645					
-	P01613	P17931					
-	P02747	Q3ZCW2					
-	P80748	P68104					
-	A0N5G5	P06576					
-	Q8IWL2	Q5T749					
-	Q9BYE4	P05091					
-	P06681	O60814					
-	Q6MZX7	P37837					
-		P22531					
-		P03973					
-		P63167					
-		P05783					
-		P50990					
-		P15880					
-		P35908					
-		P07476					
-		P49862					
\ No newline at end of file
+<!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>
--- a/venn_diagram.py	Tue Jan 14 09:14:27 2020 -0500
+++ b/venn_diagram.py	Wed May 12 16:48:05 2021 +0000
@@ -1,19 +1,20 @@
-#!/usr/bin/env python2.7
+#!/usr/bin/env python
 
-import os
-import sys
+import argparse
+import csv
 import json
-import operator
-import argparse
-import re, csv
+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
@@ -29,16 +30,17 @@
         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"]  
+    c = ["A", "B", "C", "D", "E", "F"]
     for i in range(len(inputs)):
-        input_file = inputs[i][0]        
+        input_file = inputs[i][0]
         name = inputs[i][1]
         input_type = inputs[i][2]
         title = c[i]
@@ -47,30 +49,35 @@
         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
-            
+            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":
-                        file_content = [x for x in [line[int(ncol.replace("c", ""))-1].split(";") for line in file_content[1:]]]     # gets ids from defined column
+                        # 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]] 
+                        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")        
+                    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]
-            
-        file_content = [item.strip() for sublist in file_content for item in sublist if item != '']   #flat list of list of lists, remove empty items    
+
+        # 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')
+        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
@@ -83,8 +90,9 @@
             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)))
-            yield group, list(intersected), list(difference)    
+                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):
     """
@@ -94,54 +102,59 @@
     result["name"] = {}
     for k in comp_dict.keys():
         result["name"][k] = title_dict[k]
-        
+
     result["data"] = {}
-    result["values"] = {}    
+    result["values"] = {}
     for group, intersected, difference in intersect(comp_dict):
         if len(group) == 1:
-            result["data"]["".join(group)] = difference
+            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)] = difference
-	        result["values"]["".join(group)] = len(difference)               
+            result["data"]["".join(group)] = sorted(difference)
+            result["values"]["".join(group)] = len(difference)
         elif len(group) == len(comp_dict):
-            result["data"]["".join(group)] = intersected
+            result["data"]["".join(group)] = sorted(intersected)
             result["values"]["".join(group)] = len(intersected)
 
     return result
 
-#Write intersections of input to text output file
+# 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"].iteritems() if v != [])
-    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"].iteritems() if v != [])
+    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
+    # get list names associated to each column
     column_dict = {}
-    for key in result :
-        if key in list_names :
+    for key in result:
+        if key in list_names:
             column_dict[key] = list_names[key]
-        else : 
-            keys= list(key)
+        else:
+            keys = list(key)
             column_dict[key] = "_".join([list_names[k] for k in keys])
 
-    #construct tsv
-    for key in result :
+    # construct tsv
+    for key in result:
         line = result[key]
-        if len(line) < nb_lines_max :
-            line.extend(['NA']*(nb_lines_max-len(line)))
-        line = [column_dict[key]] + line                #add header
-        lines.append(line)  
-    #transpose tsv
-    lines=zip(*lines)
-    
+        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
@@ -151,37 +164,41 @@
     write_text_venn(data)
 
     to_replace = {
-    	"series": [data],
-    	"displayStat": "true",
-    	"displaySwitch": "true",
+        "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" )
+    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]")
+    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 )
+    process(args)
--- a/venn_diagram.xml	Tue Jan 14 09:14:27 2020 -0500
+++ b/venn_diagram.xml	Wed May 12 16:48:05 2021 +0000
@@ -1,7 +1,10 @@
 <?xml version="1.0"?>
-<tool id="Jvenn" name="Venn diagram" version="2020.01.10">
+<tool id="Jvenn" name="Venn diagram" version="2021.05.12">
 	<description>[JVenn]
 	</description>
+<requirements>
+<requirement type="package" version="3.7.3">python</requirement>
+</requirements>
 	<command><![CDATA[
 		python $__tool_directory__/venn_diagram.py
 
@@ -69,8 +72,17 @@
 	                <param name="file" value="ID_Converter_FKW_Lacombe_et_al_2017_OK.txt" />
 	                <param name="header" value="true" />
 	                <param name="ncol" value="c1" />
-	                <param name="name" value="Lacombe" />
 	            </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">
@@ -78,20 +90,11 @@
 	                <param name="file" value="Mucilli.txt" />
 	                <param name="header" value="false" />
 	                <param name="ncol" value="c1" />
-	                <param name="name" value="Mucilli" />
 	            </conditional>
-	        </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" />
-	                <param name="name" value="Bredberg" />
-	            </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" />      
+	        <!-- <output name="output_text" file="Venn_text_output.txt" />       -->
 	    </test>
 	</tests>
 	<help><![CDATA[