annotate venn_diagram.xml @ 0:6f22d2726103 draft default tip

planemo upload

<?xml version="1.0"?>
<tool id="Jvenn" name="Venn diagram plotter" version="1.0">
	<description>An integrative tool for comparing up to 6 ID lists with Venn Diagrams (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 [e-mail] for any questions or concerns about the Galaxy implementation of this tool.

	</help> 
	<citations>
    </citations>
</tool>