<?xml version="1.0" encoding="UTF-8"?>
<tool id="met4j_Tab2Sbml" name="Tab2Sbml" version="1.3.0">
  <description>Create a Sbml File from a tabulated file that contains the reaction 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:1.3.0</container>
  </requirements>
  <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh convert.Tab2Sbml#if str($colid) != 'nan':
 -ci "$colid"
#end if
#if str($colformula) != 'nan':
 -cf "$colformula"
#end if
 $rp
 $mp
#if str($e):
 -e "$e"
#end if
#if str($i):
 -i "$i"
#end if
#if str($r):
 -r "$r"
#end if
 -in "$in"
#if str($id):
 -id "$id"
#end if
 $createCompartment
#if str($defaultCompartment):
 -dcpt "$defaultCompartment"
#end if
#if str($nSkip) != 'nan':
 -n "$nSkip"
#end if
 -sbml "$sbml"
]]></command>
  <inputs>
    <param argument="-ci" label="[1] number of the column where are the reaction ids" name="colid" optional="true" type="integer" value="1"/>
    <param argument="-cf" label="[2] number of the column where are the reaction formulas" name="colformula" optional="true" type="integer" value="2"/>
    <param argument="-rp" checked="false" falsevalue="" label="[deactivated] format the reaction ids in a Palsson way (R_***)" name="rp" truevalue="-rp" type="boolean" value="false"/>
    <param argument="-mp" checked="false" falsevalue="" label="[deactivated] format the metabolite ids in a Palsson way (M_***_c)" name="mp" truevalue="-mp" type="boolean" value="false"/>
    <param argument="-e" label="[_b] flag to assign metabolite as external" name="e" optional="true" type="text" value="_b">
      <sanitizer invalid_char="_">
        <valid initial="string.printable"/>
      </sanitizer>
    </param>
    <param argument="-i" label="[--&gt;] String for irreversible reaction" name="i" optional="true" type="text" value="--&gt;">
      <sanitizer invalid_char="_">
        <valid initial="string.printable"/>
      </sanitizer>
    </param>
    <param argument="-r" label="[&lt;==&gt;] String for reversible reaction" name="r" optional="true" type="text" value="&lt;==&gt;">
      <sanitizer invalid_char="_">
        <valid initial="string.printable"/>
      </sanitizer>
    </param>
    <param argument="-in" format="tsv" label="Tabulated file" name="in" optional="false" type="data" value=""/>
    <param argument="-id" label="[NA] Model id written in the SBML file" name="id" optional="true" type="text" value="NA">
      <sanitizer invalid_char="_">
        <valid initial="string.printable"/>
      </sanitizer>
    </param>
    <param argument="-cpt" checked="false" falsevalue="" label="[deactivated] Create compartment from metabolite suffixes. If this option is deactivated, only one compartment (the default compartment) will be created" name="createCompartment" truevalue="-cpt" type="boolean" value="false"/>
    <param argument="-dcpt" label="[c] Default compartment" name="defaultCompartment" optional="true" type="text" value="c">
      <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="integer" value="0"/>
  </inputs>
  <outputs>
    <data format="sbml" name="sbml"/>
  </outputs>
  <tests>
    <test>
      <param name="in" value="toy_model.tsv"/>
      <output ftype="sbml" name="sbml">
        <assert_contents>
          <is_valid_xml/>
          <has_line_matching expression=".*reaction .*" n="7"/>
          <has_line_matching expression=".*species .*" n="8"/>
        </assert_contents>
      </output>
    </test>
    <test>
      <param name="in" value="toy_model_otherColumns.tsv"/>
      <param name="colid" value="2"/>
      <param name="colformula" value="3"/>
      <output ftype="sbml" name="sbml">
        <assert_contents>
          <is_valid_xml/>
          <has_line_matching expression=".*reaction .*" n="7"/>
          <has_line_matching expression=".*species .*" n="8"/>
        </assert_contents>
      </output>
    </test>
    <test>
      <param name="in" value="toy_model_otherSigns.tsv"/>
      <param name="i" value="-&gt;"/>
      <param name="r" value="="/>
      <output ftype="sbml" name="sbml">
        <assert_contents>
          <is_valid_xml/>
          <has_line_matching expression=".*reaction .*" n="7"/>
          <has_line_matching expression=".*species .*" n="8"/>
        </assert_contents>
      </output>
    </test>
    <test>
      <param name="in" value="toy_model.tsv"/>
      <param name="rp" value="true"/>
      <param name="mp" value="true"/>
      <param name="e" value="_e"/>
      <param name="createCompartment" value="true"/>
      <output ftype="sbml" name="sbml">
        <assert_contents>
          <is_valid_xml/>
          <has_line_matching expression=".*boundaryCondition=.true.*" n="3"/>
          <has_line_matching expression=".*id=.M_A_ext_e.*" n="1"/>
          <has_line_matching expression=".*id=.R_reac2.*" n="1"/>
        </assert_contents>
      </output>
    </test>
    <test>
      <param name="in" value="toy_model.tsv"/>
      <param name="id" value="myModel"/>
      <output ftype="sbml" name="sbml">
        <assert_contents>
          <is_valid_xml/>
          <has_line_matching expression=".*myModel.*" n="1"/>
        </assert_contents>
      </output>
    </test>
  </tests>
  <help><![CDATA[Create a Sbml File from a tabulated file that contains the reaction ids and the formulas]]></help>
  <citations/>
</tool>