Mercurial > repos > metexplore > met4j
view tools/networkAnalysis/NetworkSummary/NetworkSummary.xml @ 3:6bd9aad9626d draft
planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit a078bf88575dac3d09462252eae92c24f34d0414
author | metexplore |
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date | Fri, 29 Jul 2022 13:23:40 +0000 |
parents | e69a78624877 |
children | ae4c301919c4 |
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<?xml version="1.0" encoding="UTF-8"?> <tool id="met4j_NetworkSummary" name="NetworkSummary" version="1.1.0"> <description>Create a report summarizing several graph measures characterising the structure of the network.</description> <xrefs> <xref type="bio.tools">met4j</xref> </xrefs> <requirements> <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.1.0</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.NetworkSummary -i "$inputPath" #if str($sideCompoundFile) != 'None': -s "$sideCompoundFile" #end if $skipdist $directed -o "$outputPath" ]]></command> <inputs> <param argument="-i" format="sbml" label="input SBML file" name="inputPath" optional="false" type="data" value=""/> <param argument="-s" format="" label="an optional file containing list of side compounds to ignore (recommended)" name="sideCompoundFile" optional="true" type="data" value=""/> <param argument="-sd" checked="false" falsevalue="" label="skip full distance matrix computation (quick summary)" name="skipdist" truevalue="-sd" type="boolean" value="false"/> <param argument="-d" checked="false" falsevalue="" label="use reaction direction for distances" name="directed" truevalue="-d" type="boolean" value="false"/> </inputs> <outputs> <data format="" name="outputPath"/> </outputs> <tests> <test> <param name="inputPath" value="toy_model.xml"/> <output name="outputPath"> </output> </test> </tests> <help><![CDATA[Use a metabolic network in SBML file and an optional list of side compounds, and produce a report summarizing several graph measures characterising the structure of the network.This includes (non-exhaustive list): size and order, connectivity, density, degree distribution, shortest paths length, top centrality nodes...]]></help> <citations/> </tool>