<?xml version="1.0" encoding="UTF-8"?>
<tool id="met4j_SbmlSetRefsFromFile" name="SbmlSetRefsFromFile" version="1.2.0">
  <description>Add refs to network objects from a tabulated file containing the metabolite ids and the formulas</description>
  <xrefs>
    <xref type="bio.tools">met4j</xref>
  </xrefs>
  <requirements>
    <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.2.0</container>
  </requirements>
  <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.SbmlSetRefsFromFile#if str($colRef) != 'nan':
 -cr "$colRef"
#end if
 -ref "$ref"
#if str($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="-cr" label="[2] number of the column where are the references" name="colRef" optional="true" type="integer" value="2"/>
    <param argument="-ref" label="Name of the ref. Must exist in identifiers.org" name="ref" optional="false" type="text" value="">
      <sanitizer invalid_char="_">
        <valid initial="string.printable"/>
      </sanitizer>
    </param>
    <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="refs.tsv"/>
      <param name="ref" value="InChi"/>
      <param name="o" value="METABOLITE"/>
      <output ftype="sbml" name="out">
        <assert_contents>
          <is_valid_xml/>
          <has_line_matching expression=".*C2H6O.*" n="3"/>
          <has_line_matching expression=".*C6H8O6.*" n="1"/>
        </assert_contents>
      </output>
    </test>
  </tests>
  <help><![CDATA[Add refs to network objects from a tabulated file containing the metabolite ids and the formulas
Reference name given as parameter (-ref) must correspond to an existing id the registry of  identifiers.org (https://registry.identifiers.org/registry)
The corresponding key:value pair will be written as metabolite or reaction annotation]]></help>
  <citations/>
</tool>