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view tools/convert/Sbml2Graph/Sbml2Graph.xml @ 0:dcd16521b969 draft
planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 5dab0a2d83a1fdd7a1878a50ba0f24e752505393
author | metexplore |
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date | Fri, 10 Jun 2022 10:31:34 +0000 |
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children | 9b162ee6ff8e |
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<?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>