Mercurial > repos > lcottret > met4j
diff tools/convert/Sbml2Graph/Sbml2Graph.xml @ 0:3cdcfdae8bd2 draft default tip
"planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit a58b6f8a6dde6ef64da64ee50395dc5bc848167a-dirty"
author | lcottret |
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date | Tue, 31 May 2022 07:45:16 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/convert/Sbml2Graph/Sbml2Graph.xml Tue May 31 07:45:16 2022 +0000 @@ -0,0 +1,61 @@ +<?xml version="1.0" encoding="UTF-8"?> +<tool id="met4j_Sbml2Graph" name="Sbml2Graph" version="0.11.0"> + <description>Create a graph representation of a SBML file content, and export it in graph file format.</description> + <xrefs> + <xref type="bio.tools">met4j</xref> + </xrefs> + <requirements> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:0.11.0</container> + </requirements> + <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh convert.Sbml2Graph -i "$inputPath" + $bipartite + $compound + $reaction + $tab + $gml + -o "$outputPath" +]]></command> + <inputs> + <param argument="-i" format="sbml" label="input SBML file" name="inputPath" optional="false" type="data" value=""/> + <param argument="-b" checked="false" falsevalue="" label="create bipartite graph" name="bipartite" truevalue="-b" type="boolean" value="false"/> + <param argument="-c" checked="true" falsevalue="" label="create compound graph" name="compound" truevalue="-c" type="boolean" value="true"/> + <param argument="-r" checked="false" falsevalue="" label="create reaction graph" name="reaction" truevalue="-r" type="boolean" value="false"/> + <param argument="-tab" checked="false" falsevalue="" label="export in tabulated file" name="tab" truevalue="-tab" type="boolean" value="false"/> + <param argument="-gml" checked="true" falsevalue="" label="export in GML file" name="gml" truevalue="-gml" type="boolean" value="true"/> + </inputs> + <outputs> + <data format="text" name="outputPath"/> + </outputs> + <tests> + <test> + <param name="inputPath" value="toy_model.xml"/> + <output name="outputPath"> + <assert_contents> + <has_n_lines n="101"/> + </assert_contents> + </output> + </test> + <test> + <param name="inputPath" value="toy_model.xml"/> + <param name="bipartite" value="true"/> + <param name="compound" value="false"/> + <output name="outputPath"> + <assert_contents> + <has_n_lines n="184"/> + </assert_contents> + </output> + </test> + <test> + <param name="inputPath" value="toy_model.xml"/> + <param name="reaction" value="true"/> + <param name="compound" value="false"/> + <output name="outputPath"> + <assert_contents> + <has_n_lines n="90"/> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[Create a graph representation of a SBML file content, and export it in graph file format. +The graph can be either a compound graph or a bipartite graph, and can be exported in gml or tabulated file format.]]></help> +</tool>