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comparison tools/networkAnalysis/BipartiteDistanceMatrix/BipartiteDistanceMatrix.xml @ 9:0976a6257300 draft

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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 7a6f2380fc1d
children 6a112eaf8f38
comparison
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8:1274e2a62479 9:0976a6257300
1 <?xml version="1.0" encoding="UTF-8"?> 1 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
2 <tool id="met4j_BipartiteDistanceMatrix" name="BipartiteDistanceMatrix" version="MET4J_VERSION_TEST"> 2 <tool id="met4j_BipartiteDistanceMatrix" name="BipartiteDistanceMatrix" version="develop">
3 <description>Create a compound to reactions distance matrix.</description> 3 <description>Create a compound to reactions distance matrix.</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:MET4J_VERSION_TEST</container> 8 <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop</container>
9 </requirements> 9 </requirements>
10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.BipartiteDistanceMatrix -i "$inputPath" 10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.BipartiteDistanceMatrix -i "$inputPath"
11 #if str($sideCompoundFile) != 'None': 11 #if str($sideCompoundFile) != 'None':
12 -sc "$sideCompoundFile" 12 -sc "$sideCompoundFile"
13 #end if 13 #end if
40 <outputs> 40 <outputs>
41 <data format="csv" name="outputPath"/> 41 <data format="csv" name="outputPath"/>
42 </outputs> 42 </outputs>
43 <tests/> 43 <tests/>
44 <help><![CDATA[Create a compound to reactions distance matrix. 44 <help><![CDATA[Create a compound to reactions distance matrix.
45 The distance between two nodes (metabolite or reaction) is computed as the length of the shortest path connecting the two in the bipartite graph, Bipartite graph are composed of two distinct sets of nodes and two nodes can be linked only if they are from distinct sets. 45 The distance between two nodes (metabolite or reaction) is computed as the length of the shortest path connecting the two in the bipartite graph, Bipartite graphs are composed of two distinct sets of nodes and two nodes can be linked only if they are from distinct sets.
46 Therefore a metabolite node can be linked to a reaction node if the metabolite is a substrate or product of the reaction. 46 Therefore a metabolite node can be linked to a reaction node if the metabolite is a substrate or product of the reaction.
47 An optional custom 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.Custom weighting can be provided in a file. In that case, edges without weight are ignored during path search. 47 An optional custom 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.Custom weighting can be provided in a file. In that case, edges without weight are ignored during path search.
48 If no edge weighting is set, it is recommended to provide a list of side compounds to ignore during network traversal.]]></help> 48 If no edge weighting is set, it is recommended to provide a list of side compounds to ignore during network traversal.]]></help>
49 <citations/> 49 <citations/>
50 </tool> 50 </tool>