Mercurial > repos > lnguyen > venn_diagram_plotter
diff venn_diagram.xml @ 0:6f22d2726103 draft default tip
planemo upload
| author | lnguyen |
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| date | Fri, 15 Sep 2017 09:32:19 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/venn_diagram.xml Fri Sep 15 09:32:19 2017 -0400 @@ -0,0 +1,169 @@ +<?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="'"/> + </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>