<?xml version="1.0" encoding="UTF-8"?>
<tool id="met4j_SbmlSetIdsFromFile" name="SbmlSetIdsFromFile" version="1.2.1">
  <description>Set new ids to network objects from a tabulated file containing the old ids and the new ids</description>
  <xrefs>
    <xref type="bio.tools">met4j</xref>
  </xrefs>
  <requirements>
    <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.2.1</container>
  </requirements>
  <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.SbmlSetIdsFromFile#if str($colname) != 'nan':
 -cnew "$colname"
#end if
#if str($colid):
 -ci "$colid"
#end if
 $p
 $s
#if str($o):
 -o "$o"
#end if
#if str($nSkip):
 -n "$nSkip"
#end if
 -sbml "$sbml"
#if str($tab) != 'None':
 -tab "$tab"
#end if
#if str($c):
 -c "$c"
#end if
 -out "$out"
]]></command>
  <inputs>
    <param argument="-cnew" label="[2] number of the column where are the new ids" name="colname" optional="true" type="integer" value="2"/>
    <param argument="-ci" label="[1] number of the column where are the object ids" name="colid" optional="true" type="text" value="1">
      <sanitizer invalid_char="_">
        <valid initial="string.printable"/>
      </sanitizer>
    </param>
    <param argument="-p" checked="false" falsevalue="" label="[deactivated] To match the objects in the sbml file, adds the prefix R_ to reactions and M_ to metabolites" name="p" truevalue="-p" type="boolean" value="false"/>
    <param argument="-s" checked="false" falsevalue="" label="[deactivated] To match the objects in the sbml file, adds the suffix _comparmentID to metabolites" name="s" truevalue="-s" type="boolean" value="false"/>
    <param argument="-o" label="[REACTION] Object type in the column id : REACTION;METABOLITE;GENE;PATHWAY" name="o" optional="true" type="text" value="REACTION">
      <sanitizer invalid_char="_">
        <valid initial="string.printable"/>
      </sanitizer>
    </param>
    <param argument="-n" label="[0] Number of lines to skip at the beginning of the tabulated file" name="nSkip" optional="true" type="text" value="0">
      <sanitizer invalid_char="_">
        <valid initial="string.printable"/>
      </sanitizer>
    </param>
    <param argument="-sbml" format="sbml" label="Original sbml file" name="sbml" optional="false" type="data" value=""/>
    <param argument="-tab" format="tsv" label="Tabulated file" name="tab" optional="true" type="data" value=""/>
    <param argument="-c" label="[#] Comment String in the tabulated file. The lines beginning by this string won't be read" name="c" optional="true" type="text" value="#">
      <sanitizer invalid_char="_">
        <valid initial="string.printable"/>
      </sanitizer>
    </param>
  </inputs>
  <outputs>
    <data format="sbml" name="out"/>
  </outputs>
  <tests>
    <test>
      <param name="sbml" value="toy_model.xml"/>
      <param name="tab" value="idMetabolites.tsv"/>
      <param name="o" value="METABOLITE"/>
      <output ftype="sbml" name="out">
        <assert_contents>
          <is_valid_xml/>
          <has_line_matching expression=".*id=.metaboliteA.*" n="1"/>
          <has_line_matching expression=".*id=.metaboliteB.*" n="1"/>
        </assert_contents>
      </output>
    </test>
    <test>
      <param name="sbml" value="toy_model.xml"/>
      <param name="tab" value="idReactions.tsv"/>
      <output ftype="sbml" name="out">
        <assert_contents>
          <is_valid_xml/>
          <has_line_matching expression=".*id=.reaction1.*" n="1"/>
          <has_line_matching expression=".*id=.reaction2.*" n="1"/>
        </assert_contents>
      </output>
    </test>
    <test>
      <param name="sbml" value="XF_network.sbml"/>
      <param name="tab" value="idPathways.tsv"/>
      <param name="o" value="PATHWAY"/>
      <output ftype="sbml" name="out">
        <assert_contents>
          <is_valid_xml/>
          <has_line_matching expression=".*groups:id=.CEB.*" n="1"/>
          <has_line_matching expression=".*groups:id=.NSP.*" n="1"/>
        </assert_contents>
      </output>
    </test>
    <test>
      <param name="sbml" value="XF_network.sbml"/>
      <param name="tab" value="idGenes.tsv"/>
      <param name="o" value="GENE"/>
      <output ftype="sbml" name="out">
        <assert_contents>
          <is_valid_xml/>
          <has_line_matching expression=".*fbc:id=.G1.*" n="1"/>
          <has_line_matching expression=".*fbc:id=.G2.*" n="1"/>
        </assert_contents>
      </output>
    </test>
    <test>
      <param name="sbml" value="XF_network.sbml"/>
      <param name="tab" value="idCompartments.tsv"/>
      <param name="o" value="COMPARTMENT"/>
      <output ftype="sbml" name="out">
        <assert_contents>
          <is_valid_xml/>
          <has_line_matching expression=".*id=.cytosol.*" n="1"/>
          <has_line_matching expression=".*id=.extra.*" n="1"/>
        </assert_contents>
      </output>
    </test>
  </tests>
  <help><![CDATA[Set new ids to network objects from a tabulated file containing the old ids and the new ids
The ids must correspond between the tabulated file and the SBML file.
If prefix or suffix is different in the SBML file, use the -p or the -s options.
]]></help>
  <citations/>
</tool>