--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/venn_diagram.xml	Sun Nov 26 19:09:40 2017 -0500
@@ -0,0 +1,170 @@
+<?xml version="1.0"?>
+<tool id="Jvenn" name="Venn diagram" version="1.0">
+	<description>compare lists plotting Venn Diagram (based on Jvenn).
+	</description>
+	<command><![CDATA[
+		python $__tool_directory__/venn_diagram.py
+
+		#for $i, $s in enumerate($series)
+		    --input
+		    #if $s.se.input == "file"
+		        "$s.se.file" "$s.se.name" "file" "$s.se.header" "$s.se.ncol"
+		    #else
+                "$s.se.list" "$s.se.name" "list"
+ 		    #end if
+		#end for 
+		--summary "$output_summary"
+	]]></command>
+	<inputs>
+		<!-- Files -->
+		<repeat name="series" title="Lists to compare" min="2" max="6" >
+            <conditional name="se" >
+                    <param type="select" name="input" label="Please provide your identifiers" help="Copy/paste or ID list from a file (e.g. table)" >
+                        <option value="list">Copy/paste your identifiers </option>
+                        <option value="file">Input file containing your identifiers</option>
+                        
+                    </param>
+                    <when value="file">
+                        <param type="data" name="file" format="txt,tabular" label="Choose a file that contains your list of IDs" />
+                        <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does your input file contain header?" />
+		            	<param type="text" name="ncol" value="c1" label="Please specify the column where you would like to apply the comparison" help ='For example, fill in "c1" if you want to filter the first column' />
+		            	<param type="text" name="name" value="" label="Please enter the name of this list" help="This name will be displayed on venn diagram" />
+                    </when>
+                    <when value="list">
+                        <param type="text" name="list" label="Copy/paste your identifiers" help='IDs must be separated by spaces into the form field, for example: P31946 P62258' >
+                            <sanitizer>
+                                <valid initial="string.printable">
+                                    <remove value="&apos;"/>
+                                </valid>
+                                <mapping initial="none">
+                                    <add source="&apos;" target="__sq__"/>
+                                </mapping>
+                            </sanitizer>
+                        </param>
+                        <param type="text" name="name" value="" label="Please enter the name of this list" help="This name will be displayed on venn diagram" />
+                    </when>
+                </conditional>
+		</repeat>
+	</inputs>
+	<outputs>
+		<data format="html" name="output_summary" label="Venn diagram" from_work_dir="venn_diagram_summary.html" />
+		<data format="tabular" name="output_text" label="Venn diagram text output" from_work_dir="venn_diagram_text_output.txt" />
+	</outputs>
+	<tests>
+	    <test>
+	        <repeat name="series">
+	            <conditional name="se">
+	                <param name="input" value="mq_file" />
+	                <param name="mq_file" value="DESeq.txt" />
+	                <param name="header" value="false" />
+	                <param name="ncol" value="c1" />
+	                <param name="name" value="DESeq" />
+	            </conditional>
+	        </repeat>
+	        <repeat name="series">
+	            <conditional name="se">
+	                <param name="input" value="mq_file" />
+	                <param name="mq_file" value="FQ.txt" />
+	                <param name="header" value="false" />
+	                <param name="ncol" value="c1" />
+	                <param name="name" value="FQ" />
+	            </conditional>
+	        </repeat>
+	        <repeat name="series">
+	            <conditional name="se">
+	                <param name="input" value="mq_file" />
+	                <param name="mq_file" value="RPKM.txt" />
+	                <param name="header" value="false" />
+	                <param name="ncol" value="c1" />
+	                <param name="name" value="RPKM" />
+	            </conditional>
+	        </repeat>
+	        <repeat name="series">
+	            <conditional name="se">
+	                <param name="input" value="mq_file" />
+	                <param name="mq_file" value="TC.txt" />
+	                <param name="header" value="false" />
+	                <param name="ncol" value="c1" />
+	                <param name="name" value="TC" />
+	            </conditional>
+	        </repeat>
+	        <repeat name="series">
+	            <conditional name="se">
+	                <param name="input" value="mq_file" />
+	                <param name="mq_file" value="TMM.txt" />
+	                <param name="header" value="false" />
+	                <param name="ncol" value="c1" />
+	                <param name="name" value="TMM" />
+	            </conditional>
+	        </repeat>
+	        <repeat name="series">
+	            <conditional name="se">
+	                <param name="input" value="mq_file" />
+	                <param name="mq_file" value="UQ.txt" />
+	                <param name="header" value="false" />
+	                <param name="ncol" value="c1" />
+	                <param name="name" value="UQ" />
+	            </conditional>
+	        </repeat>
+	        <output name="output_summary" file="venn_diagram_summary.html" />
+	        <output name="output_text" file="venn_diagram_text_output.txt" />
+	                
+	    </test>
+	</tests>
+	<help>
+
+This tool draw a venn diagram from lists/files using Jvenn plug-in (http://jvenn.toulouse.inra.fr/app/index.html). It also creates output files that contain common or specific elements between query and each compared lists/files.
+
+**Inputs**
+
+* **Query file:** A file containing different information of proteins, could be output of previous components.
+
+* **File of a list of IDs:** .TXT format, each line contains 1 ID
+    
+    AMY1A
+    
+ 	ALB
+ 	
+ 	IGKC
+ 	
+ 	CSTA
+ 	
+ 	IGHA1
+ 	
+ 	ACTG1
+
+* **List of IDs:** IDs separated by a space
+    AMY1A ALB IGKC CSTA IGHA1 ACTG1
+
+If you choose a file, it is necessary to specify the column where you would like to perform the comparison.
+
+**Outputs**
+
+* **Summary file** (venn_diagram_summary.html):
+    Venn diagram: Could be downloaded as image (PNG, SVG)
+
+* **Venn text output file**
+    A text file containing common/specific elements among compared lists/files.
+    
+-----
+
+.. class:: infomark
+
+**Authors**
+
+Philippe Bardou, Jérôme Mariette, Frédéric Escudié, Christophe Djemiel and Christophe Klopp. jvenn: an interactive Venn diagram viewer. BMC Bioinformatics 2014, 15:293 doi:10.1186/1471-2105-15-293
+
+.. class:: infomark
+
+**Galaxy integration**
+
+T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR
+
+Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit,Migale Bioinformatics platform
+
+Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool.
+
+	</help> 
+	<citations>
+    </citations>
+</tool>