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comparison build/tools/ExtractSubReactionNetwork/ExtractSubReactionNetwork.xml @ 10:6a112eaf8f38 draft

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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
comparison
equal deleted inserted replaced
9:0976a6257300 10:6a112eaf8f38
1 <?xml version="1.0" encoding="UTF-8" standalone="no"?> 1 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
2 <tool id="met4j_ExtractSubReactionNetwork" name="ExtractSubReactionNetwork" version="develop"> 2 <tool id="met4j_ExtractSubReactionNetwork" name="ExtractSubReactionNetwork" version="2.0.0">
3 <description>Create a subnetwork from a metabolic network in SBML format, and two files containing lists of 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 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:develop</container> 8 <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0</container>
9 </requirements> 9 </requirements>
10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.ExtractSubReactionNetwork -i "$inputPath" 10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.ExtractSubReactionNetwork -i "$inputPath"
11 -s "$sourcePath" 11 -s "$sourcePath"
12 $undirected 12 $undirected
13 -t "$targetPath" 13 -t "$targetPath"
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
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60 <param name="inputPath" value="toy_model.xml"/> 57 <param name="inputPath" value="toy_model.xml"/>
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64 <param name="sourcePath" value="seeds.txt"/> 58 <param name="sourcePath" value="seeds.txt"/>
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68 <param name="targetPath" value="targets.txt"/> 59 <param name="targetPath" value="targets.txt"/>
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72 <param name="sideCompoundFile" value="sides.txt"/> 60 <param name="sideCompoundFile" value="sides.txt"/>
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76 <param name="format" value="gml"/> 61 <param name="format" value="gml"/>
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80 <output ftype="txt" name="output"> 62 <output ftype="txt" name="output">
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84 <assert_contents> 63 <assert_contents>
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88 <has_line_matching expression=".*node.*" n="3"/> 64 <has_line_matching expression=".*node.*" n="3"/>
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92 <has_line_matching expression=".*edge.*" n="2"/> 65 <has_line_matching expression=".*edge.*" n="2"/>
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96 </assert_contents> 66 </assert_contents>
97
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100 </output> 67 </output>
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104 </test> 68 </test>
105 </tests> 69 </tests>
106 <help><![CDATA[Create a subnetwork from a metabolic network in SBML format, and two files containing lists of reactions of interests ids, one per row, plus one file of the same format containing side compounds ids. 70 <help><![CDATA[Create a subnetwork from a metabolic network in SBML format, and two files containing lists of reactions of interests ids, one per row, plus one file of the same format containing side compounds ids.
107 The subnetwork corresponds to the part of the network that connects reactions from the first list to reactions from the second list. 71 The subnetwork corresponds to the part of the network that connects reactions from the first list to reactions from the second list.
108 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, reaction graph often lacks weighting policy for edge relevance. In order to ensure appropriate network density, a list of side compounds to ignore for linking reactions must be provided. An optional edge weight file, if available, can also be used.]]></help> 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, reaction graph often lacks weighting policy for edge relevance. In order to ensure appropriate network density, a list of side compounds to ignore for linking reactions must be provided. An optional edge weight file, if available, can also be used.]]></help>