met4j: build/tools/ReactionDistanceMatrix/ReactionDistanceMatrix.xml comparison

comparison build/tools/ReactionDistanceMatrix/ReactionDistanceMatrix.xml @ 9:0976a6257300 draft

planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 05db35f63cadb9d56dafff594a3507c59cd85273

author	metexplore
date	Fri, 31 Jan 2025 18:28:53 +0000
parents	1274e2a62479
children	6a112eaf8f38

comparison

equal deleted inserted replaced

-:1274e2a62479
+:0976a6257300
-<?xml version="1.0" encoding="UTF-8"?>
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
-<tool id="met4j_ReactionDistanceMatrix" name="ReactionDistanceMatrix" version="1.5.0">
+<tool id="met4j_ReactionDistanceMatrix" name="ReactionDistanceMatrix" version="develop">
 <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:1.5.0</container>
+<container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop</container>
 </requirements>
 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.ReactionDistanceMatrix -i "$inputPath"
 #if str($sideCompoundFile) != 'None':
 -sc "$sideCompoundFile"
 #end if
 <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>
 <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.

Mercurial > repos > metexplore > met4j

comparison build/tools/ReactionDistanceMatrix/ReactionDistanceMatrix.xml @ 9:0976a6257300 draft