Mercurial > repos > metexplore > met4j_reactiondistancematrix
diff ReactionDistanceMatrix.xml @ 3:392f9fe363e8 draft default tip
planemo upload for repository https://forge.inrae.fr/metexplore/met4j-galaxy commit e757d0398a8407d983f1ef3f900b31cafc26e170
| author | metexplore |
|---|---|
| date | Wed, 21 Jan 2026 15:31:23 +0000 |
| parents | d05c0c639108 |
| children |
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--- a/ReactionDistanceMatrix.xml Fri Nov 21 10:22:11 2025 +0000 +++ b/ReactionDistanceMatrix.xml Wed Jan 21 15:31:23 2026 +0000 @@ -35,95 +35,7 @@ <outputs> <data format="csv" name="outputPath"/> </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> + <tests/> <help><![CDATA[Create a reaction to reaction distance matrix. The distance between two reactions is computed as the length of the shortest path connecting the two in the reaction graph, where two reactions are linked if they produce a metabolite consumed by the other or the other way around. An optional edge weighting can be used, turning the distances into the sum of edge weights in the lightest path, rather than the length of the shortest path.The default weighting use target's degree squared. Alternatively, custom weighting can be provided in a file. In that case, edges without weight are ignored during path search.