<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<tool id="met4j_GetEntities" name="GetEntities" version="2.0.0">
  <description>Parse a SBML file to return a list of entities composing the network: metabolites, reactions, genes and others.</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 attributes.GetEntities -i "$sbml"
 $printMetabolites
 $printReactions
 $printCompartments
 $printPathways
 $printGenes
 $noTypeCol
 -o "$outputFile"
]]></command>
  <inputs>
    <param argument="-i" format="sbml" label="Input SBML file" name="sbml" optional="false" type="data" value=""/>
    <param argument="-m" checked="false" falsevalue="" label="Extract Metabolites" name="printMetabolites" truevalue="-m" type="boolean" value="false"/>
    <param argument="-r" checked="false" falsevalue="" label="Extract Reactions" name="printReactions" truevalue="-r" type="boolean" value="false"/>
    <param argument="-c" checked="false" falsevalue="" label="Extract Compartments" name="printCompartments" truevalue="-c" type="boolean" value="false"/>
    <param argument="-p" checked="false" falsevalue="" label="Extract Pathways" name="printPathways" truevalue="-p" type="boolean" value="false"/>
    <param argument="-g" checked="false" falsevalue="" label="Extract Genes" name="printGenes" truevalue="-g" type="boolean" value="false"/>
    <param argument="-nt" checked="false" falsevalue="" label="Do not write type column" name="noTypeCol" truevalue="-nt" type="boolean" value="false"/>
  </inputs>
  <outputs>
    <data format="tsv" name="outputFile"/>
  </outputs>
  <tests>
    <test>
      <param name="sbml" value="Human-GEM_pathways.xml"/>
      <output ftype="tsv" name="outputFile">
        <assert_contents>
          <has_text_matching expression="GENE" n="86"/>
          <has_text_matching expression="METABOLITE" n="111"/>
          <has_text_matching expression="REACTION" n="75"/>
          <has_text_matching expression="PATHWAY" n="3"/>
          <has_text_matching expression="COMPARTMENT" n="5"/>
        </assert_contents>
      </output>
    </test>
    <test>
      <param name="sbml" value="Human-GEM_pathways.xml"/>
      <param name="printReactions" value="true"/>
      <param name="printMetabolites" value="true"/>
      <param name="printGenes" value="true"/>
      <param name="printCompartments" value="true"/>
      <param name="noTypeCol" value="true"/>
      <output ftype="tsv" name="outputFile">
        <assert_contents>
          <has_n_lines n="277"/>
        </assert_contents>
      </output>
    </test>
  </tests>
  <help><![CDATA[Parse a SBML file to return a list of entities composing the network: metabolites, reactions, genes and others.The output file is a tabulated file with two columns, one with entity identifiers, and one with the entity type. If no entity type is selected, all of them are returned by default. Only identifiers are written, attributes can be extracted from dedicated apps or from the Sbml2Tab app.]]></help>
  <citations/>
</tool>