Mercurial > repos > metexplore > met4j
comparison build/tools/Sbml2Graph/Sbml2Graph.xml @ 11:40c15b7467f1 draft default tip
planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 61dbdbae896d18b519a470e056cb8b4f98394518
| author | metexplore |
|---|---|
| date | Thu, 13 Feb 2025 15:08:22 +0000 |
| parents | 6a112eaf8f38 |
| children |
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| 10:6a112eaf8f38 | 11:40c15b7467f1 |
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| 1 <?xml version="1.0" encoding="UTF-8" standalone="no"?> | 1 <?xml version="1.0" encoding="UTF-8" standalone="no"?> |
| 2 <tool id="met4j_Sbml2Graph" name="Sbml2Graph" version="2.0.0"> | 2 <tool id="met4j_Sbml2Graph" name="Sbml2Graph" version="2.0.1"> |
| 3 <description>Create a graph representation of a SBML file content, and export it in graph file format.</description> | 3 <description>Create a graph representation of a SBML file content, and export it in graph file format.</description> |
| 4 <xrefs> | 4 <xrefs> |
| 5 <xref type="bio.tools">met4j</xref> | 5 <xref type="bio.tools">met4j</xref> |
| 6 </xrefs> | 6 </xrefs> |
| 7 <requirements> | 7 <requirements> |
| 8 <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0</container> | 8 <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.1</container> |
| 9 </requirements> | 9 </requirements> |
| 10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh convert.Sbml2Graph -i "$inputPath" | 10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh convert.Sbml2Graph -i "$inputPath" |
| 11 $bipartite | 11 $bipartite |
| 12 $compound | 12 $compound |
| 13 $reaction | 13 $reaction |
| 32 <outputs> | 32 <outputs> |
| 33 <data format="txt" name="output"/> | 33 <data format="txt" name="output"/> |
| 34 </outputs> | 34 </outputs> |
| 35 <tests> | 35 <tests> |
| 36 <test> | 36 <test> |
| 37 | |
| 37 <param name="inputPath" value="toy_model.xml"/> | 38 <param name="inputPath" value="toy_model.xml"/> |
| 39 | |
| 38 <param name="format" value="gml"/> | 40 <param name="format" value="gml"/> |
| 41 | |
| 39 <output name="output"> | 42 <output name="output"> |
| 43 | |
| 40 <assert_contents> | 44 <assert_contents> |
| 45 | |
| 41 <has_line_matching expression=".*node.*" n="8"/> | 46 <has_line_matching expression=".*node.*" n="8"/> |
| 47 | |
| 42 <has_line_matching expression=".*edge.*" n="9"/> | 48 <has_line_matching expression=".*edge.*" n="9"/> |
| 49 | |
| 43 </assert_contents> | 50 </assert_contents> |
| 51 | |
| 44 </output> | 52 </output> |
| 53 | |
| 45 </test> | 54 </test> |
| 46 <test> | 55 <test> |
| 56 | |
| 47 <param name="inputPath" value="toy_model.xml"/> | 57 <param name="inputPath" value="toy_model.xml"/> |
| 58 | |
| 48 <param name="bipartite" value="true"/> | 59 <param name="bipartite" value="true"/> |
| 60 | |
| 49 <param name="compound" value="false"/> | 61 <param name="compound" value="false"/> |
| 62 | |
| 50 <param name="format" value="gml"/> | 63 <param name="format" value="gml"/> |
| 64 | |
| 51 <output name="output"> | 65 <output name="output"> |
| 66 | |
| 52 <assert_contents> | 67 <assert_contents> |
| 68 | |
| 53 <has_line_matching expression=".*node.*" n="15"/> | 69 <has_line_matching expression=".*node.*" n="15"/> |
| 70 | |
| 54 <has_line_matching expression=".*edge.*" n="17"/> | 71 <has_line_matching expression=".*edge.*" n="17"/> |
| 72 | |
| 55 </assert_contents> | 73 </assert_contents> |
| 74 | |
| 56 </output> | 75 </output> |
| 76 | |
| 57 </test> | 77 </test> |
| 58 <test> | 78 <test> |
| 79 | |
| 59 <param name="inputPath" value="toy_model.xml"/> | 80 <param name="inputPath" value="toy_model.xml"/> |
| 81 | |
| 60 <param name="reaction" value="true"/> | 82 <param name="reaction" value="true"/> |
| 83 | |
| 61 <param name="compound" value="false"/> | 84 <param name="compound" value="false"/> |
| 85 | |
| 62 <param name="format" value="gml"/> | 86 <param name="format" value="gml"/> |
| 87 | |
| 63 <output name="output"> | 88 <output name="output"> |
| 89 | |
| 64 <assert_contents> | 90 <assert_contents> |
| 91 | |
| 65 <has_line_matching expression=".*node.*" n="7"/> | 92 <has_line_matching expression=".*node.*" n="7"/> |
| 93 | |
| 66 <has_line_matching expression=".*edge.*" n="8"/> | 94 <has_line_matching expression=".*edge.*" n="8"/> |
| 95 | |
| 67 </assert_contents> | 96 </assert_contents> |
| 97 | |
| 68 </output> | 98 </output> |
| 99 | |
| 69 </test> | 100 </test> |
| 70 </tests> | 101 </tests> |
| 71 <help><![CDATA[Create a graph representation of a SBML file content, and export it in graph file format. | 102 <help><![CDATA[Create a graph representation of a SBML file content, and export it in graph file format. |
| 72 The graph can be either a compound graph, a reaction graph or a bipartite graph, and can be exported in gml or tabulated file format.]]></help> | 103 The graph can be either a compound graph, a reaction graph or a bipartite graph, and can be exported in gml or tabulated file format.]]></help> |
| 73 <citations> | 104 <citations> |