Mercurial > repos > tduigou > rpreport
view rpreport.xml @ 0:d09a51507aaf draft
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author | tduigou |
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date | Mon, 14 Feb 2022 14:23:00 +0000 |
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children | 3ea8aa1e94b4 |
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<tool id="rpreport" name="Pathways HTML Report" version="@TOOL_VERSION@" profile="19.09"> <description>Generates HTML report to explore the main characteristics of pathways predicted with RetroPath suite</description> <macros> <token name="@TOOL_VERSION@">5.12.1</token> </macros> <requirements> <requirement type="package" version="@TOOL_VERSION@">rptools</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ #if str($input_type_conditional.input_type) == "sbml": cd /tmp && #set input_folder="tmp_folder" mkdir -p '$input_folder' && #for $input in $input_type_conditional.input_sbml.keys(): ln -sfn $input_type_conditional.input_sbml[$input] '$input_folder/$input'; #end for python -m rptools.rpreport -d '$input_folder' #elif str($input_type_conditional.input_type) == "tar": python -m rptools.rpreport '${input_type_conditional.input_tar}' #end if '$html_file.files_path' && cp '$html_file.files_path'/index.html '$html_file' ]]></command> <inputs> <conditional name="input_type_conditional"> <param name="input_type" type="select" label="Source SBML format"> <option value="tar" selected="True">TAR</option> <option value="sbml">Collection</option> </param> <when value="tar"> <param name="input_tar" type="data" format="tar" label="Source SBML" /> </when> <when value="sbml"> <param name="input_sbml" type="data_collection" format="xml" collection_type="list" label="Source SBML" /> </when> </conditional> </inputs> <outputs> <data name="html_file" format="html" label="Pathways HTML Report"/> </outputs> <tests> <test> <!-- test 2: check if identical html output is produced (tar input) --> <conditional name="input_type_conditional"> <param name="input_type" value="tar"/> <param name="input_tar" value="input_rpSBML.tar" /> </conditional> <output name="html_file" file="rpreport_output.html" compare="diff"/> </test> </tests> <help><![CDATA[ rpReport ========= Generates HTML pages to explore the main characteristics (thermodynamics, fluxes, number of metabolic steps, reaction rule score) of pathways predicted with RetroPath suite Input ----- Required: * **source_path**: (string) Path to a tar archive (default) or folder (using '-d' option) containing rpSBML file(s). Output ------ * **output_folder**: (string) Output folder where report file(s) will be generated. Project Links --------------------- * `GitHub <https://github.com/brsynth/rptools>`_ Version ---------- 5.12.1 Authors ------- * **Olivier Telle** Acknowledgments --------------- * Thomas Duigou * Joan Hérisson Licence ------- `MIT <https://github.com/brsynth/rptools/blob/master/LICENSE>`_ ]]></help> </tool>