Mercurial > repos > metexplore > met4j

comparison build/tools/ExtractSubBipNetwork/ExtractSubBipNetwork.xml @ 11:40c15b7467f1 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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
comparison
equal deleted inserted replaced
10:6a112eaf8f38 11:40c15b7467f1
1 <?xml version="1.0" encoding="UTF-8" standalone="no"?> 1 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
2 <tool id="met4j_ExtractSubBipNetwork" name="ExtractSubBipNetwork" version="2.0.0"> 2 <tool id="met4j_ExtractSubBipNetwork" name="ExtractSubBipNetwork" version="2.0.1">
3 <description>Create a subnetwork from a metabolic network in SBML format, and two files containing lists of compounds and/or reactions of interests ids, one per row, plus one file of the same format containing side compounds ids.</description> 3 <description>Create a subnetwork from a metabolic network in SBML format, and two files containing lists of compounds and/or reactions of interests ids, one per row, plus one file of the same format containing side compounds ids.</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 networkAnalysis.ExtractSubBipNetwork -i "$inputPath" 10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.ExtractSubBipNetwork -i "$inputPath"
11 -s "$sourcePath" 11 -s "$sourcePath"
12 -t "$targetPath" 12 -t "$targetPath"
13 $undirected 13 $undirected
52 <outputs> 52 <outputs>
53 <data format="txt" name="output"/> 53 <data format="txt" name="output"/>
54 </outputs> 54 </outputs>
55 <tests> 55 <tests>
56 <test> 56 <test>
57
57 <param name="inputPath" value="toy_model.xml"/> 58 <param name="inputPath" value="toy_model.xml"/>
59
58 <param name="sourcePath" value="seeds.txt"/> 60 <param name="sourcePath" value="seeds.txt"/>
61
59 <param name="targetPath" value="targets.txt"/> 62 <param name="targetPath" value="targets.txt"/>
63
60 <param name="sideCompoundFile" value="sc.txt"/> 64 <param name="sideCompoundFile" value="sc.txt"/>
65
61 <param name="format" value="gml"/> 66 <param name="format" value="gml"/>
67
62 <output ftype="txt" name="output"> 68 <output ftype="txt" name="output">
69
63 <assert_contents> 70 <assert_contents>
71
64 <has_line_matching expression=".*node.*" n="5"/> 72 <has_line_matching expression=".*node.*" n="5"/>
73
65 <has_line_matching expression=".*edge.*" n="4"/> 74 <has_line_matching expression=".*edge.*" n="4"/>
75
66 </assert_contents> 76 </assert_contents>
77
67 </output> 78 </output>
79
68 </test> 80 </test>
69 </tests> 81 </tests>
70 <help><![CDATA[Create a subnetwork from a metabolic network in SBML format, and two files containing lists of compounds and/or reactions of interests ids, one per row, plus one file of the same format containing side compounds ids. 82 <help><![CDATA[Create a subnetwork from a metabolic network in SBML format, and two files containing lists of compounds and/or reactions of interests ids, one per row, plus one file of the same format containing side compounds ids.
71 The subnetwork corresponds to the part of the network that connects reactions and compounds from the first list to reactions and compounds from the second list. 83 The subnetwork corresponds to the part of the network that connects reactions and compounds from the first list to reactions and compounds from the second list.
72 Sources and targets list can have elements in common. The connecting part can be defined as the union of shortest or k-shortest paths between sources and targets, or the Steiner tree connecting them. Contrary to compound graph, bipartite graph often lacks weighting policy for edge relevance. In order to ensure appropriate network density, a list of side compounds and blocked reactions to ignore during path build must be provided. An optional edge weight file, if available, can also be used.]]></help> 84 Sources and targets list can have elements in common. The connecting part can be defined as the union of shortest or k-shortest paths between sources and targets, or the Steiner tree connecting them. Contrary to compound graph, bipartite graph often lacks weighting policy for edge relevance. In order to ensure appropriate network density, a list of side compounds and blocked reactions to ignore during path build must be provided. An optional edge weight file, if available, can also be used.]]></help>