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annotate build/tools/PathwayNet/PathwayNet.xml @ 7:1436e9cde9c9 draft

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planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 1d31a48bf8328b7a3ad9910971d24b9f453459c5
author metexplore
date Tue, 04 Jul 2023 10:21:26 +0000
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1 <?xml version="1.0" encoding="UTF-8"?>
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2 <tool id="met4j_PathwayNet" name="PathwayNet" version="1.4.0">
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3 <description>Creation of a Pathway Network representation of a SBML file content</description>
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4 <xrefs>
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5 <xref type="bio.tools">met4j</xref>
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6 </xrefs>
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7 <requirements>
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1436e9cde9c9 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 1d31a48bf8328b7a3ad9910971d24b9f453459c5
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8 <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.4.0</container>
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9 </requirements>
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10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.PathwayNet -s "$inputPath"
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11 #if str($inputSide) != 'None':
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12 -sc "$inputSide"
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13 #end if
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14 $removeIsolated
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15 $onlySourcesAndSinks
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16 #if str($weightFile) != 'None':
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17 -cw "$weightFile"
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18 #end if
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19 $connectors
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20 $asMatrix
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21 -o "$outputPath"
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22 ]]></command>
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23 <inputs>
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24 <param argument="-s" format="sbml" label="input SBML file" name="inputPath" optional="false" type="data" value=""/>
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25 <param argument="-sc" format="txt" label="input Side compound file (recommended)" name="inputSide" optional="true" type="data" value=""/>
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26 <param argument="-ri" checked="false" falsevalue="" label="remove isolated nodes" name="removeIsolated" truevalue="-ri" type="boolean" value="false"/>
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27 <param argument="-oss" checked="false" falsevalue="" label="consider only metabolites that are source or sink in the pathway (i.e non-intermediary compounds)" name="onlySourcesAndSinks" truevalue="-oss" type="boolean" value="false"/>
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28 <param argument="-cw" format="tsv" label="an optional file containing weights for pathway pairs" name="weightFile" optional="true" type="data" value=""/>
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29 <param argument="-ncw" checked="false" falsevalue="" label="set number of connecting compounds as weight" name="connectors" truevalue="-ncw" type="boolean" value="false"/>
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30 <param argument="-am" checked="false" falsevalue="" label="export as matrix (implies simple graph conversion). Default export as GML file" name="asMatrix" truevalue="-am" type="boolean" value="false"/>
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31 </inputs>
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32 <outputs>
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33 <data format="gml" name="outputPath"/>
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34 </outputs>
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35 <tests/>
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36 <help><![CDATA[Genome-scale metabolic networks are often partitioned into metabolic pathways. Pathways are frequently considered independently despite frequent coupling in their activity due to shared metabolites. In order to decipher the interconnections linking overlapping pathways, this app proposes the creation of "Pathway Network", where two pathways are linked if they share compounds.]]></help>
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37 <citations/>
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38 </tool>