<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<tool id="met4j_GetReactantsFromReactions" name="GetReactantsFromReactions" version="2.0.0">
  <description>Get reactant lists from a list of reactions and a SBML file.</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.GetReactantsFromReactions -i "$sbml"
 -r "$reactionFile"
#if str($sep):
 -sep "$sep"
#end if
 $hasHeader
#if str($i) != 'nan':
 -col "$i"
#end if
 $printSubstrates
 $printProducts
 -o "$outputFile"
]]></command>
  <inputs>
    <param argument="-i" format="sbml" label="Input SBML file" name="sbml" optional="false" type="data" value=""/>
    <param argument="-r" format="tsv" label="Input Reaction file" name="reactionFile" optional="false" type="data" value=""/>
    <param argument="-sep" label="Separator in reaction file" name="sep" optional="true" type="text" value="&#9;">
      <sanitizer invalid_char="_">
        <valid initial="string.printable"/>
      </sanitizer>
    </param>
    <param argument="-header" checked="false" falsevalue="" label="Skip reaction file header" name="hasHeader" truevalue="-header" type="boolean" value="false"/>
    <param argument="-col" label="Column number in reaction file (first as 1)" name="i" optional="true" type="integer" value="1"/>
    <param argument="-s" checked="false" falsevalue="" label="Extract substrates only" name="printSubstrates" truevalue="-s" type="boolean" value="false"/>
    <param argument="-p" checked="false" falsevalue="" label="Extract products only" name="printProducts" truevalue="-p" type="boolean" value="false"/>
  </inputs>
  <outputs>
    <data format="tsv" name="outputFile"/>
  </outputs>
  <tests>
    <test>
      <param name="sbml" value="XF_network.sbml"/>
      <param name="reactionFile" value="XF_network_R_Seed.tab"/>
      <output ftype="tsv" name="outputFile">
        <assert_contents>
          <has_text_matching expression="R_GLUN" n="4"/>
          <has_text_matching expression="R_ACGS" n="5"/>
        </assert_contents>
      </output>
    </test>
    <test>
      <param name="sbml" value="XF_network.sbml"/>
      <param name="reactionFile" value="XF_network_R_Seed.tab"/>
      <param name="printSubstrates" value="true"/>
      <output ftype="tsv" name="outputFile">
        <assert_contents>
          <has_text_matching expression="R_GLUN" n="2"/>
          <has_text_matching expression="R_ACGS" n="5"/>
        </assert_contents>
      </output>
    </test>
    <test>
      <param name="sbml" value="XF_network.sbml"/>
      <param name="reactionFile" value="XF_network_R_Seed.tab"/>
      <param name="printProducts" value="true"/>
      <output ftype="tsv" name="outputFile">
        <assert_contents>
          <has_text_matching expression="R_GLUN" n="2"/>
          <has_text_matching expression="R_ACGS" n="5"/>
        </assert_contents>
      </output>
    </test>
  </tests>
  <help><![CDATA[Get reactant lists from a list of reactions and a Sbml file. Output a tab-separated file with one row per reactant, reaction identifiers in first column, reactant identifiers in second column. It can provides substrates, products, or both (by default). In the case of reversible reactions, all reactants are considered as both substrates and products]]></help>
  <citations/>
</tool>