Mercurial > repos > metexplore > met4j
diff tools/networkAnalysis/NetworkSummary/NetworkSummary.xml @ 0:dcd16521b969 draft
planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 5dab0a2d83a1fdd7a1878a50ba0f24e752505393
author | metexplore |
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date | Fri, 10 Jun 2022 10:31:34 +0000 |
parents | |
children | 9b162ee6ff8e |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/networkAnalysis/NetworkSummary/NetworkSummary.xml Fri Jun 10 10:31:34 2022 +0000 @@ -0,0 +1,35 @@ +<?xml version="1.0" encoding="UTF-8"?> +<tool id="met4j_NetworkSummary" name="NetworkSummary" version="0.11.0"> + <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:0.11.0</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> +</tool>