<?xml version="1.0" encoding="UTF-8"?>
<tool id="met4j_SbmlSetFormulasFromFile" name="SbmlSetFormulasFromFile" version="0.11.0">
  <description>Set Formula to network metabolites 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:0.11.0</container>
  </requirements>
  <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.SbmlSetFormulasFromFile#if str($colformula) != 'nan':
 -cf "$colformula"
#end if
#if str($colid) != 'nan':
 -ci "$colid"
#end if
 $p
 $s
#if str($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="-cf" label="[2] number of the column where are the formulas" name="colformula" optional="true" type="integer" value="2"/>
    <param argument="-ci" label="[1] number of the column where are the metabolite ids" name="colid" optional="true" type="integer" value="1"/>
    <param argument="-p" checked="false" falsevalue="" label="[deactivated] To match the objects in the sbml file, adds the prefix M_ to metabolite ids" 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="-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="formula.tsv"/>
      <output ftype="sbml" name="out">
        <assert_contents>
          <is_valid_xml/>
          <has_line_matching expression=".*CH6O6.*" n="2"/>
          <has_line_matching expression=".*CH12O4.*" n="2"/>
        </assert_contents>
      </output>
    </test>
    <test expect_failure="true">
      <param name="sbml" value="toy_model.xml"/>
      <param name="tab" value="formulaBad.tsv"/>
    </test>
  </tests>
  <help><![CDATA[Set Formula to network metabolites from a tabulated file containing the metabolite ids and the formulas
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.
The formula will be written in the SBML file in two locations:+
- in the metabolite notes (e.g. <p>formula: C16H29O2</p>

- as a fbc attribute (e.g. fbc:chemicalFormula="C16H29O2")]]></help>
</tool>