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comparison build/tools/SideCompoundsScan/SideCompoundsScan.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
children
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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_SideCompoundsScan" name="SideCompoundsScan" version="2.0.0"> 2 <tool id="met4j_SideCompoundsScan" name="SideCompoundsScan" version="2.0.1">
3 <description>Scan a network to identify side compounds.</description> 3 <description>Scan a network to identify side compounds.</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.SideCompoundsScan -i "$inputPath" 10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.SideCompoundsScan -i "$inputPath"
11 $sideOnly 11 $sideOnly
12 $noReportValue 12 $noReportValue
13 #if str($degree): 13 #if str($degree):
48 <outputs> 48 <outputs>
49 <data format="tsv" name="outputPath"/> 49 <data format="tsv" name="outputPath"/>
50 </outputs> 50 </outputs>
51 <tests> 51 <tests>
52 <test> 52 <test>
53
53 <param name="inputPath" value="XF_network.sbml"/> 54 <param name="inputPath" value="XF_network.sbml"/>
55
54 <output ftype="tsv" name="outputPath"> 56 <output ftype="tsv" name="outputPath">
57
55 <assert_contents> 58 <assert_contents>
59
56 <has_n_lines n="1108"/> 60 <has_n_lines n="1108"/>
61
57 <has_n_columns n="4"/> 62 <has_n_columns n="4"/>
63
58 </assert_contents> 64 </assert_contents>
65
59 </output> 66 </output>
67
60 </test> 68 </test>
61 <test> 69 <test>
70
62 <param name="inputPath" value="XF_network.sbml"/> 71 <param name="inputPath" value="XF_network.sbml"/>
72
63 <param name="noReportValue" value="true"/> 73 <param name="noReportValue" value="true"/>
74
64 <output ftype="tsv" name="outputPath"> 75 <output ftype="tsv" name="outputPath">
76
65 <assert_contents> 77 <assert_contents>
78
66 <has_n_lines n="6"/> 79 <has_n_lines n="6"/>
80
67 <has_n_columns n="1"/> 81 <has_n_columns n="1"/>
82
68 </assert_contents> 83 </assert_contents>
84
69 </output> 85 </output>
86
70 </test> 87 </test>
71 </tests> 88 </tests>
72 <help><![CDATA[Scan a network to identify side compounds. 89 <help><![CDATA[Scan a network to identify side compounds.
73 Side compounds are metabolites of small relevance for topological analysis. Their definition can be quite subjective and varies between sources. 90 Side compounds are metabolites of small relevance for topological analysis. Their definition can be quite subjective and varies between sources.
74 Side compounds tend to be ubiquitous and not specific to a particular biochemical or physiological process.Compounds usually considered as side compounds include water, atp or carbon dioxide. By being involved in many reactions and thus connected to many compounds, they tend to significantly lower the average shortest path distances beyond expected metabolic relatedness. 91 Side compounds tend to be ubiquitous and not specific to a particular biochemical or physiological process.Compounds usually considered as side compounds include water, atp or carbon dioxide. By being involved in many reactions and thus connected to many compounds, they tend to significantly lower the average shortest path distances beyond expected metabolic relatedness.