| Previous changeset 2:310645d4c5e6 (2022-11-18) |
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Commit message:
planemo upload commit 3bc34bfc82850daa2229724c396dcd9454039273-dirty |
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removed:
rpreport.xml |
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| diff -r 310645d4c5e6 -r 4525f388f3ac rpreport.xml --- a/rpreport.xml Fri Nov 18 16:18:02 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,91 +0,0 @@ -<tool id="rpreport" name="Pathways HTML Report" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09"> - <description>Explore the main characteristics of pathways predicted with RetroPath suite</description> - <macros> - <token name="@VERSION_SUFFIX@">0</token> - <token name="@TOOL_VERSION@">6.0.1</token> - </macros> - <requirements> - <requirement type="package" version="@TOOL_VERSION@">rptools</requirement> - </requirements> - <command detect_errors="exit_code"><![CDATA[ - #if str($input_type_conditional.input_type) == "sbml": - #set input_folder="tmp_folder" - mkdir -p '$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" help="rpSBML file(s) containing pathways predicted with RetroPath suite in TAR format"/> - </when> - <when value="sbml"> - <param name="input_sbml" type="data_collection" format="sbml" collection_type="list" label="Source SBML" help="Collection of rpSBML files containing pathways predicted with RetroPath suite"/> - </when> - </conditional> - </inputs> - <outputs> - <data name="html_file" format="html" label="Pathways HTML Report"/> - </outputs> - <tests> - <test> - <!-- test 1: 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 <https://www.sciencedirect.com/science/article/pii/S1096717617301337>`_. - - -Input ------ - -Required: - -* **Source SBML**: rpSBML file(s) containing pathways predicted with RetroPath suite. - -Output ------- - -* **Pathways HTML Report**: Pathways HTML Report - -Project Links ---------------------- - -* `GitHub <https://github.com/brsynth/rptools>`_ - -Acknowledgments ---------------- - -* Thomas Duigou -* Joan Hérisson - -Licence -------- - -`MIT <https://github.com/brsynth/rptools/blob/master/LICENSE>`_ - ]]></help> - <creator> - <person givenName="Olivier" familyName="Telle" email="olivier.telle@inrae.fr" /> - </creator> -</tool> \ No newline at end of file |