<?xml version="1.0" encoding="UTF-8"?>
<tool id="met4j_Sbml2Graph" name="Sbml2Graph" version="1.0.1">
  <description>Create a graph representation of a SBML file content, and export it in graph file format.</description>
  <xrefs>
    <xref type="bio.tools">met4j</xref>
  </xrefs>
  <requirements>
    <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.0.1</container>
  </requirements>
  <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh convert.Sbml2Graph -i "$inputPath"
 $bipartite
 $compound
 $reaction
 $tab
 $gml
 -o "$outputPath"
]]></command>
  <inputs>
    <param argument="-i" format="sbml" label="input SBML file" name="inputPath" optional="false" type="data" value=""/>
    <param argument="-b" checked="false" falsevalue="" label="create bipartite graph" name="bipartite" truevalue="-b" type="boolean" value="false"/>
    <param argument="-c" checked="true" falsevalue="" label="create compound graph" name="compound" truevalue="-c" type="boolean" value="true"/>
    <param argument="-r" checked="false" falsevalue="" label="create reaction graph" name="reaction" truevalue="-r" type="boolean" value="false"/>
    <param argument="-tab" checked="false" falsevalue="" label="export in tabulated file" name="tab" truevalue="-tab" type="boolean" value="false"/>
    <param argument="-gml" checked="true" falsevalue="" label="export in GML file" name="gml" truevalue="-gml" type="boolean" value="true"/>
  </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 n="101"/>
        </assert_contents>
      </output>
    </test>
    <test>
      <param name="inputPath" value="toy_model.xml"/>
      <param name="bipartite" value="true"/>
      <param name="compound" value="false"/>
      <output name="outputPath">
        <assert_contents>
          <has_n_lines n="184"/>
        </assert_contents>
      </output>
    </test>
    <test>
      <param name="inputPath" value="toy_model.xml"/>
      <param name="reaction" value="true"/>
      <param name="compound" value="false"/>
      <output name="outputPath">
        <assert_contents>
          <has_n_lines n="90"/>
        </assert_contents>
      </output>
    </test>
  </tests>
  <help><![CDATA[Create a graph representation of a SBML file content, and export it in graph file format.
The graph can be either a compound graph or a bipartite graph, and can be exported in gml or tabulated file format.]]></help>
  <citations/>
</tool>