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comparison tools/networkAnalysis/SideCompoundsScan/SideCompoundsScan.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_SideCompoundsScan" name="SideCompoundsScan" version="develop"> 2 <tool id="met4j_SideCompoundsScan" name="SideCompoundsScan" version="2.0.0">
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: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.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>
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64 <param name="inputPath" value="XF_network.sbml"/> 53 <param name="inputPath" value="XF_network.sbml"/>
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76 <output ftype="tsv" name="outputPath"> 54 <output ftype="tsv" name="outputPath">
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88 <assert_contents> 55 <assert_contents>
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100 <has_n_lines n="1108"/> 56 <has_n_lines n="1108"/>
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112 <has_n_columns n="4"/> 57 <has_n_columns n="4"/>
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124 </assert_contents> 58 </assert_contents>
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136 </output> 59 </output>
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148 </test> 60 </test>
149 <test> 61 <test>
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161 <param name="inputPath" value="XF_network.sbml"/> 62 <param name="inputPath" value="XF_network.sbml"/>
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173 <param name="noReportValue" value="true"/> 63 <param name="noReportValue" value="true"/>
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185 <output ftype="tsv" name="outputPath"> 64 <output ftype="tsv" name="outputPath">
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197 <assert_contents> 65 <assert_contents>
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209 <has_n_lines n="6"/> 66 <has_n_lines n="6"/>
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221 <has_n_columns n="1"/> 67 <has_n_columns n="1"/>
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233 </assert_contents> 68 </assert_contents>
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245 </output> 69 </output>
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257 </test> 70 </test>
258 </tests> 71 </tests>
259 <help><![CDATA[Scan a network to identify side compounds. 72 <help><![CDATA[Scan a network to identify side compounds.
260 Side compounds are metabolites of small relevance for topological analysis. Their definition can be quite subjective and varies between sources. 73 Side compounds are metabolites of small relevance for topological analysis. Their definition can be quite subjective and varies between sources.
261 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. 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.