Mercurial > repos > metexplore > met4j
comparison build/tools/Sbml2Graph/Sbml2Graph.xml @ 6:7a6f2380fc1d draft
planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
| author | metexplore |
|---|---|
| date | Wed, 17 May 2023 13:26:37 +0000 |
| parents | |
| children | 1436e9cde9c9 |
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| 5:35c9abcd8934 | 6:7a6f2380fc1d |
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| 1 <?xml version="1.0" encoding="UTF-8"?> | |
| 2 <tool id="met4j_Sbml2Graph" name="Sbml2Graph" version="1.3.0"> | |
| 3 <description>Create a graph representation of a SBML file content, and export it in graph file format.</description> | |
| 4 <xrefs> | |
| 5 <xref type="bio.tools">met4j</xref> | |
| 6 </xrefs> | |
| 7 <requirements> | |
| 8 <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.3.0</container> | |
| 9 </requirements> | |
| 10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh convert.Sbml2Graph -i "$inputPath" | |
| 11 $bipartite | |
| 12 $compound | |
| 13 $reaction | |
| 14 $tab | |
| 15 $gml | |
| 16 -o "$outputPath" | |
| 17 ]]></command> | |
| 18 <inputs> | |
| 19 <param argument="-i" format="sbml" label="input SBML file" name="inputPath" optional="false" type="data" value=""/> | |
| 20 <param argument="-b" checked="false" falsevalue="" label="create bipartite graph" name="bipartite" truevalue="-b" type="boolean" value="false"/> | |
| 21 <param argument="-c" checked="true" falsevalue="" label="create compound graph" name="compound" truevalue="-c" type="boolean" value="true"/> | |
| 22 <param argument="-r" checked="false" falsevalue="" label="create reaction graph" name="reaction" truevalue="-r" type="boolean" value="false"/> | |
| 23 <param argument="-tab" checked="false" falsevalue="" label="export in tabulated file" name="tab" truevalue="-tab" type="boolean" value="false"/> | |
| 24 <param argument="-gml" checked="true" falsevalue="" label="export in GML file" name="gml" truevalue="-gml" type="boolean" value="true"/> | |
| 25 </inputs> | |
| 26 <outputs> | |
| 27 <data format="txt" name="outputPath"/> | |
| 28 </outputs> | |
| 29 <tests> | |
| 30 <test> | |
| 31 <param name="inputPath" value="toy_model.xml"/> | |
| 32 <output name="outputPath"> | |
| 33 <assert_contents> | |
| 34 <has_n_lines n="101"/> | |
| 35 </assert_contents> | |
| 36 </output> | |
| 37 </test> | |
| 38 <test> | |
| 39 <param name="inputPath" value="toy_model.xml"/> | |
| 40 <param name="bipartite" value="true"/> | |
| 41 <param name="compound" value="false"/> | |
| 42 <output name="outputPath"> | |
| 43 <assert_contents> | |
| 44 <has_n_lines n="184"/> | |
| 45 </assert_contents> | |
| 46 </output> | |
| 47 </test> | |
| 48 <test> | |
| 49 <param name="inputPath" value="toy_model.xml"/> | |
| 50 <param name="reaction" value="true"/> | |
| 51 <param name="compound" value="false"/> | |
| 52 <output name="outputPath"> | |
| 53 <assert_contents> | |
| 54 <has_n_lines n="90"/> | |
| 55 </assert_contents> | |
| 56 </output> | |
| 57 </test> | |
| 58 </tests> | |
| 59 <help><![CDATA[Create a graph representation of a SBML file content, and export it in graph file format. | |
| 60 The graph can be either a compound graph or a bipartite graph, and can be exported in gml or tabulated file format.]]></help> | |
| 61 <citations/> | |
| 62 </tool> |