Mercurial > repos > metexplore > met4j
diff tools/networkAnalysis/ReactionDistanceMatrix/ReactionDistanceMatrix.xml @ 10:6a112eaf8f38 draft
planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 71071300dd662ad01bd064abcf6866a192eeea95
| author | metexplore |
|---|---|
| date | Mon, 03 Feb 2025 15:59:46 +0000 |
| parents | 0976a6257300 |
| children | 40c15b7467f1 |
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--- a/tools/networkAnalysis/ReactionDistanceMatrix/ReactionDistanceMatrix.xml Fri Jan 31 18:28:53 2025 +0000 +++ b/tools/networkAnalysis/ReactionDistanceMatrix/ReactionDistanceMatrix.xml Mon Feb 03 15:59:46 2025 +0000 @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8" standalone="no"?> -<tool id="met4j_ReactionDistanceMatrix" name="ReactionDistanceMatrix" version="develop"> +<tool id="met4j_ReactionDistanceMatrix" name="ReactionDistanceMatrix" version="2.0.0"> <description>Create a reaction to reaction distance matrix.</description> <xrefs> <xref type="bio.tools">met4j</xref> </xrefs> <requirements> - <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.ReactionDistanceMatrix -i "$inputPath" #if str($sideCompoundFile) != 'None': @@ -38,982 +38,91 @@ </outputs> <tests> <test> - - - - - - - - - - - <param name="inputPath" value="toy_model.xml"/> - - - - - - - - - - - <output ftype="csv" name="outputPath"> - - - - - - - - - - - <assert_contents> - - - - - - - - - - - <has_n_lines n="8"/> - - - - - - - - - - - <has_line_matching expression="id,reac1,reac2,reac3,reac4,reac5,reac6,reac7" n="1"/> - - - - - - - - - - - <has_line_matching expression="reac1,0.0,1.0,1.0,2.0,3.0,Infinity,Infinity" n="1"/> - - - - - - - - - - - <has_line_matching expression="reac2,Infinity,0.0,1.0,1.0,2.0,Infinity,Infinity" n="1"/> - - - - - - - - - - - </assert_contents> - - - - - - - - - - - </output> - - - - - - - - - - - </test> <test> - - - - - - - - - - - <param name="inputPath" value="toy_model.xml"/> - - - - - - - - - - - <param name="undirected" value="true"/> - - - - - - - - - - - <output ftype="csv" name="outputPath"> - - - - - - - - - - - <assert_contents> - - - - - - - - - - - <has_n_lines n="8"/> - - - - - - - - - - - <has_line_matching expression="id,reac1,reac2,reac3,reac4,reac5,reac6,reac7" n="1"/> - - - - - - - - - - - <has_line_matching expression="reac1,0.0,1.0,1.0,2.0,3.0,5.0,4.0" n="1"/> - - - - - - - - - - - <has_line_matching expression="reac2,1.0,0.0,1.0,1.0,2.0,4.0,3.0" n="1"/> - - - - - - - - - - - </assert_contents> - - - - - - - - - - - </output> - - - - - - - - - - - </test> <test> - - - - - - - - - - - <param name="inputPath" value="toy_model.xml"/> - - - - - - - - - - - <param name="undirected" value="true"/> - - - - - - - - - - - <param name="sideCompoundFile" value="sides.txt"/> - - - - - - - - - - - <output ftype="csv" name="outputPath"> - - - - - - - - - - - <assert_contents> - - - - - - - - - - - <has_n_lines n="8"/> - - - - - - - - - - - <has_line_matching expression="id,reac1,reac2,reac3,reac4,reac5,reac6,reac7" n="1"/> - - - - - - - - - - - <has_line_matching expression="reac1,0.0,1.0,1.0,2.0,3.0,5.0,4.0" n="1"/> - - - - - - - - - - - <has_line_matching expression="reac2,1.0,0.0,1.0,2.0,3.0,5.0,4.0" n="1"/> - - - - - - - - - - - <has_line_matching expression="reac3,1.0,1.0,0.0,1.0,2.0,4.0,3.0" n="1"/> - - - - - - - - - - - <has_line_matching expression="reac4,2.0,2.0,1.0,0.0,1.0,3.0,2.0" n="1"/> - - - - - - - - - - - </assert_contents> - - - - - - - - - - - </output> - - - - - - - - - - - </test> <test> - - - - - - - - - - - <param name="inputPath" value="toy_model.xml"/> - - - - - - - - - - - <param name="undirected" value="true"/> - - - - - - - - - - - <param name="rExclude" value="rexclude.txt"/> - - - - - - - - - - - <output ftype="csv" name="outputPath"> - - - - - - - - - - - <assert_contents> - - - - - - - - - - - <has_n_lines n="6"/> - - - - - - - - - - - <has_line_matching expression="id,reac1,reac2,reac3,reac4,reac5" n="1"/> - - - - - - - - - - - <has_line_matching expression="reac1,0.0,1.0,1.0,2.0,3.0" n="1"/> - - - - - - - - - - - <has_line_matching expression="reac2,1.0,0.0,1.0,1.0,2.0" n="1"/> - - - - - - - - - - - <has_line_matching expression="reac3,1.0,1.0,0.0,1.0,2.0" n="1"/> - - - - - - - - - - - <has_line_matching expression="reac4,2.0,1.0,1.0,0.0,1.0" n="1"/> - - - - - - - - - - - <has_line_matching expression="reac5,3.0,2.0,2.0,1.0,0.0" n="1"/> - - - - - - - - - - - </assert_contents> - - - - - - - - - - - </output> - - - - - - - - - - - </test> <test> - - - - - - - - - - - <param name="inputPath" value="toy_model.xml"/> - - - - - - - - - - - <param name="undirected" value="true"/> - - - - - - - - - - - <param name="sideCompoundFile" value="sides.txt"/> - - - - - - - - - - - <param name="rExclude" value="rexclude.txt"/> - - - - - - - - - - - <output ftype="csv" name="outputPath"> - - - - - - - - - - - <assert_contents> - - - - - - - - - - - <has_n_lines n="6"/> - - - - - - - - - - - <has_line_matching expression="id,reac1,reac2,reac3,reac4,reac5" n="1"/> - - - - - - - - - - - <has_line_matching expression="reac1,0.0,1.0,1.0,2.0,3.0" n="1"/> - - - - - - - - - - - <has_line_matching expression="reac2,1.0,0.0,1.0,2.0,3.0" n="1"/> - - - - - - - - - - - <has_line_matching expression="reac3,1.0,1.0,0.0,1.0,2.0" n="1"/> - - - - - - - - - - - <has_line_matching expression="reac4,2.0,2.0,1.0,0.0,1.0" n="1"/> - - - - - - - - - - - <has_line_matching expression="reac5,3.0,3.0,2.0,1.0,0.0" n="1"/> - - - - - - - - - - - </assert_contents> - - - - - - - - - - - </output> - - - - - - - - - - - </test> <test> - - - - - - - - - - - <param name="inputPath" value="toy_model.xml"/> - - - - - - - - - - - <param name="sideCompoundFile" value="sides.txt"/> - - - - - - - - - - - <param name="rExclude" value="rexclude.txt"/> - - - - - - - - - - - <output ftype="csv" name="outputPath"> - - - - - - - - - - - <assert_contents> - - - - - - - - - - - <has_n_lines n="6"/> - - - - - - - - - - - <has_line_matching expression="id,reac1,reac2,reac3,reac4,reac5" n="1"/> - - - - - - - - - - - <has_line_matching expression="reac1,0.0,1.0,1.0,2.0,3.0" n="1"/> - - - - - - - - - - - <has_line_matching expression="reac2,Infinity,0.0,1.0,2.0,3.0" n="1"/> - - - - - - - - - - - <has_line_matching expression="reac3,Infinity,Infinity,0.0,1.0,2.0" n="1"/> - - - - - - - - - - - <has_line_matching expression="reac4,Infinity,Infinity,Infinity,0.0,1.0" n="1"/> - - - - - - - - - - - <has_line_matching expression="reac5,Infinity,Infinity,Infinity,Infinity,0.0" n="1"/> - - - - - - - - - - - </assert_contents> - - - - - - - - - - - </output> - - - - - - - - - - - </test> </tests> <help><![CDATA[Create a reaction to reaction distance matrix.