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

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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
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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_ExtractSubNetwork" name="ExtractSubNetwork" version="2.0.0"> 2 <tool id="met4j_ExtractSubNetwork" name="ExtractSubNetwork" version="2.0.1">
3 <description>Create a subnetwork from a metabolic network in SBML format, and two files containing lists of compounds of interests ids, one per row.</description> 3 <description>Create a subnetwork from a metabolic network in SBML format, and two files containing lists of compounds of interests ids, one per row.</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.ExtractSubNetwork -i "$inputPath" 10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.ExtractSubNetwork -i "$inputPath"
11 -s "$sourcePath" 11 -s "$sourcePath"
12 -t "$targetPath" 12 -t "$targetPath"
13 #if str($sideCompoundFile) != 'None': 13 #if str($sideCompoundFile) != 'None':
54 <outputs> 54 <outputs>
55 <data format="txt" name="output"/> 55 <data format="txt" name="output"/>
56 </outputs> 56 </outputs>
57 <tests> 57 <tests>
58 <test> 58 <test>
59
59 <param name="inputPath" value="toy_model.xml"/> 60 <param name="inputPath" value="toy_model.xml"/>
61
60 <param name="sourcePath" value="seeds.txt"/> 62 <param name="sourcePath" value="seeds.txt"/>
63
61 <param name="targetPath" value="targets.txt"/> 64 <param name="targetPath" value="targets.txt"/>
65
62 <param name="format" value="gml"/> 66 <param name="format" value="gml"/>
67
63 <output ftype="txt" name="output"> 68 <output ftype="txt" name="output">
69
64 <assert_contents> 70 <assert_contents>
71
65 <has_line_matching expression=".*node.*" n="3"/> 72 <has_line_matching expression=".*node.*" n="3"/>
73
66 <has_line_matching expression=".*edge.*" n="2"/> 74 <has_line_matching expression=".*edge.*" n="2"/>
75
67 </assert_contents> 76 </assert_contents>
77
68 </output> 78 </output>
79
69 </test> 80 </test>
70 </tests> 81 </tests>
71 <help><![CDATA[Create a subnetwork from a metabolic network in SBML format, and two files containing lists of compounds of interests ids, one per row. 82 <help><![CDATA[Create a subnetwork from a metabolic network in SBML format, and two files containing lists of compounds of interests ids, one per row.
72 The subnetwork corresponds to the part of the network that connects compounds from the first list to compounds from the second list. 83 The subnetwork corresponds to the part of the network that connects compounds from the first list to compounds from the second list.
73 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. The relevance of considered path can be increased by weighting the edges using degree squared, chemical similarity (require InChI or SMILES annotations) or any provided weighting. 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. The relevance of considered path can be increased by weighting the edges using degree squared, chemical similarity (require InChI or SMILES annotations) or any provided weighting.
85
74 See previous works on subnetwork extraction for parameters recommendations.]]></help> 86 See previous works on subnetwork extraction for parameters recommendations.]]></help>
75 <citations> 87 <citations>
88 <citation type="doi">10.1093/nar/gki437</citation>
89 <citation type="doi">10.1093/bioinformatics/btg217</citation>
76 <citation type="doi">10.1093/bib/bbv115</citation> 90 <citation type="doi">10.1093/bib/bbv115</citation>
77 <citation type="doi">10.1016/j.biosystems.2011.05.004</citation> 91 <citation type="doi">10.1016/j.biosystems.2011.05.004</citation>
92 <citation type="doi">10.1093/bioinformatics/bti116</citation>
78 <citation type="doi">10.1016/j.jmb.2005.09.079</citation> 93 <citation type="doi">10.1016/j.jmb.2005.09.079</citation>
79 <citation type="doi">10.1093/bioinformatics/btu760</citation> 94 <citation type="doi">10.1093/bioinformatics/btu760</citation>
80 <citation type="doi">10.1093/nar/gki437</citation>
81 <citation type="doi">10.1093/bioinformatics/bti116</citation>
82 <citation type="doi">10.1093/bioinformatics/btg217</citation>
83 </citations> 95 </citations>
84 </tool> 96 </tool>