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comparison tools/networkAnalysis/ExtractSubNetwork/ExtractSubNetwork.xml @ 2:e69a78624877 draft

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planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit cb957f5d5540a48293fe8487c0cfad78ab439d7c
author metexplore
date Tue, 19 Jul 2022 14:20:07 +0000
parents 9b162ee6ff8e
children 6bd9aad9626d
comparison
equal deleted inserted replaced
1:9b162ee6ff8e 2:e69a78624877
1 <?xml version="1.0" encoding="UTF-8"?> 1 <?xml version="1.0" encoding="UTF-8"?>
2 <tool id="met4j_ExtractSubNetwork" name="ExtractSubNetwork" version="0.12.0"> 2 <tool id="met4j_ExtractSubNetwork" name="ExtractSubNetwork" version="1.0.1">
3 <description>Create a subnetwork from a GSMN in SBML format, and two files containing lists of compounds of interests ids, one per row.</description> 3 <description>Create a subnetwork from a GSMN 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:0.12.0</container> 8 <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.0.1</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':
26 $st 26 $st
27 -o "$outputPath" 27 -o "$outputPath"
28 ]]></command> 28 ]]></command>
29 <inputs> 29 <inputs>
30 <param argument="-i" format="sbml" label="input SBML file" name="inputPath" optional="false" type="data" value=""/> 30 <param argument="-i" format="sbml" label="input SBML file" name="inputPath" optional="false" type="data" value=""/>
31 <param argument="-s" format="text" label="input sources txt file" name="sourcePath" optional="false" type="data" value=""/> 31 <param argument="-s" format="txt" label="input sources txt file" name="sourcePath" optional="false" type="data" value=""/>
32 <param argument="-t" format="text" label="input targets txt file" name="targetPath" optional="false" type="data" value=""/> 32 <param argument="-t" format="txt" label="input targets txt file" name="targetPath" optional="false" type="data" value=""/>
33 <param argument="-sc" format="text" label="an optional file containing list of side compounds to ignore" name="sideCompoundFile" optional="true" type="data" value=""/> 33 <param argument="-sc" format="txt" label="an optional file containing list of side compounds to ignore" name="sideCompoundFile" optional="true" type="data" value=""/>
34 <param argument="-dw" checked="false" falsevalue="" label="penalize traversal of hubs by using degree square weighting" name="degree" truevalue="-dw" type="boolean" value="false"/> 34 <param argument="-dw" checked="false" falsevalue="" label="penalize traversal of hubs by using degree square weighting" name="degree" truevalue="-dw" type="boolean" value="false"/>
35 <param argument="-cw" format="tsv" label="an optional file containing weights for compound pairs" name="weightFile" optional="true" type="data" value=""/> 35 <param argument="-cw" format="tsv" label="an optional file containing weights for compound pairs" name="weightFile" optional="true" type="data" value=""/>
36 <param argument="-sw" checked="false" falsevalue="" label="penalize traversal of non-relevant edges by using chemical similarity weighting" name="chemicalSim" truevalue="-sw" type="boolean" value="false"/> 36 <param argument="-sw" checked="false" falsevalue="" label="penalize traversal of non-relevant edges by using chemical similarity weighting" name="chemicalSim" truevalue="-sw" type="boolean" value="false"/>
37 <param argument="-u" checked="false" falsevalue="" label="Ignore reaction direction" name="undirected" truevalue="-u" type="boolean" value="false"/> 37 <param argument="-u" checked="false" falsevalue="" label="Ignore reaction direction" name="undirected" truevalue="-u" type="boolean" value="false"/>
38 <param argument="-tab" checked="false" falsevalue="" label="Export in tabulated file instead of .GML" name="asTable" truevalue="-tab" type="boolean" value="false"/> 38 <param argument="-tab" checked="false" falsevalue="" label="Export in tabulated file instead of .GML" name="asTable" truevalue="-tab" type="boolean" value="false"/>