<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<tool id="met4j_NetworkSummary" name="NetworkSummary" version="2.0.0">
  <description>Create a report summarizing several graph measures characterising the structure of a metabolic network.</description>
  <xrefs>
    <xref type="bio.tools">met4j</xref>
  </xrefs>
  <requirements>
    <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0</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="txt" 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="txt" name="outputPath"/>
  </outputs>
  <tests>
    <test>
      <param name="inputPath" value="toy_model.xml"/>
      <output name="outputPath">
        <assert_contents>
          <has_n_lines min="1"/>
        </assert_contents>
      </output>
    </test>
  </tests>
  <help><![CDATA[Create a report summarizing several graph measures characterising the structure of a metabolic network.
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>
