<?xml version="1.0" encoding="UTF-8"?>
<tool id="met4j_PathwayNet" name="PathwayNet" version="MET4J_VERSION_TEST">
  <description>Creation of a Pathway Network representation of a SBML file content</description>
  <xrefs>
    <xref type="bio.tools">met4j</xref>
  </xrefs>
  <requirements>
    <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:MET4J_VERSION_TEST</container>
  </requirements>
  <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.PathwayNet -s "$inputPath"
#if str($inputSide) != 'None':
 -sc "$inputSide"
#end if
 $removeIsolated
 $onlySourcesAndSinks
#if str($weightFile) != 'None':
 -cw "$weightFile"
#end if
 $connectors
 $asMatrix
 -o "$outputPath"
]]></command>
  <inputs>
    <param argument="-s" format="sbml" label="input SBML file" name="inputPath" optional="false" type="data" value=""/>
    <param argument="-sc" format="txt" label="input Side compound file (recommended)" name="inputSide" optional="true" type="data" value=""/>
    <param argument="-ri" checked="false" falsevalue="" label="remove isolated nodes" name="removeIsolated" truevalue="-ri" type="boolean" value="false"/>
    <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"/>
    <param argument="-cw" format="tsv" label="an optional file containing weights for pathway pairs" name="weightFile" optional="true" type="data" value=""/>
    <param argument="-ncw" checked="false" falsevalue="" label="set number of connecting compounds as weight" name="connectors" truevalue="-ncw" type="boolean" value="false"/>
    <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"/>
  </inputs>
  <outputs>
    <data format="gml" name="outputPath"/>
  </outputs>
  <tests/>
  <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>
  <citations/>
</tool>