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comparison tools/networkAnalysis/DistanceMatrix/DistanceMatrix.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
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1:9b162ee6ff8e 2:e69a78624877
1 <?xml version="1.0" encoding="UTF-8"?> 1 <?xml version="1.0" encoding="UTF-8"?>
2 <tool id="met4j_DistanceMatrix" name="DistanceMatrix" version="0.12.0"> 2 <tool id="met4j_DistanceMatrix" name="DistanceMatrix" version="1.0.1">
3 <description>Create a compound to compound distance matrix.</description> 3 <description>Create a compound to compound distance matrix.</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.DistanceMatrix -i "$inputPath" 10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.DistanceMatrix -i "$inputPath"
11 #if str($sideCompoundFile) != 'None': 11 #if str($sideCompoundFile) != 'None':
12 -sc "$sideCompoundFile" 12 -sc "$sideCompoundFile"
13 #end if 13 #end if
21 $undirected 21 $undirected
22 -o "$outputPath" 22 -o "$outputPath"
23 ]]></command> 23 ]]></command>
24 <inputs> 24 <inputs>
25 <param argument="-i" format="sbml" label="input SBML file" name="inputPath" optional="false" type="data" value=""/> 25 <param argument="-i" format="sbml" label="input SBML file" name="inputPath" optional="false" type="data" value=""/>
26 <param argument="-sc" format="text" label="an optional file containing list of side compounds to ignore" name="sideCompoundFile" optional="true" type="data" value=""/> 26 <param argument="-sc" format="txt" label="an optional file containing list of side compounds to ignore" name="sideCompoundFile" optional="true" type="data" value=""/>
27 <param argument="-s" format="text" label="an optional file containing list of compounds of interest. The returned distance matrix contains only the corresponding rows and columns" name="seedFile" optional="true" type="data" value=""/> 27 <param argument="-s" format="txt" label="an optional file containing list of compounds of interest. The returned distance matrix contains only the corresponding rows and columns" name="seedFile" optional="true" type="data" value=""/>
28 <param argument="-dw" checked="false" falsevalue="" label="penalize traversal of hubs by using degree square weighting (-w must not be set)" name="degree" truevalue="-dw" type="boolean" value="false"/> 28 <param argument="-dw" checked="false" falsevalue="" label="penalize traversal of hubs by using degree square weighting (-w must not be set)" name="degree" truevalue="-dw" type="boolean" value="false"/>
29 <param argument="-w" format="tsv" label="an optional file containing weights for compound pairs" name="weightFile" optional="true" type="data" value=""/> 29 <param argument="-w" format="tsv" label="an optional file containing weights for compound pairs" name="weightFile" optional="true" type="data" value=""/>
30 <param argument="-u" checked="false" falsevalue="" label="Ignore reaction direction" name="undirected" truevalue="-u" type="boolean" value="false"/> 30 <param argument="-u" checked="false" falsevalue="" label="Ignore reaction direction" name="undirected" truevalue="-u" type="boolean" value="false"/>
31 </inputs> 31 </inputs>
32 <outputs> 32 <outputs>