<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<tool id="met4j_Tab2Sbml" name="Tab2Sbml" version="@TOOL_VERSION@">
  <description>Create a Sbml File from a tabulated file that contains the reaction ids and the formulas</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="bio_tools"/>
  <expand macro="requirements"/>
  <command detect_errors="exit_code"><![CDATA[met4j convert.Tab2Sbml#if str($colid) != 'nan':
 -ci "$colid"
#end if
#if str($colformula) != 'nan':
 -cf "$colformula"
#end if
#if str($i):
 -irr "$i"
#end if
#if str($r):
 -rev "$r"
#end if
 -i "$in"
#if str($id):
 -id "$id"
#end if
#if str($defaultCompartment):
 -dcpt "$defaultCompartment"
#end if
 $usePalssonConvention
#if str($boundaryCompartment):
 -b "$boundaryCompartment"
#end if
#if str($nSkip) != 'nan':
 -n "$nSkip"
#end if
 $keepGoing
 -o "$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="-irr" 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="-rev" 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="-i" 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="-dcpt" label="[c] Default compartment" name="defaultCompartment" optional="true" type="text" value="c">
      <sanitizer invalid_char="_">
        <valid initial="string.printable"/>
      </sanitizer>
    </param>
    <param argument="-M_c" checked="false" falsevalue="" label="[false] Use Palsson et al. convention: compartment suffix in metabolite ids with _ separator" name="usePalssonConvention" truevalue="-M_c" type="boolean" value="false"/>
    <param argument="-b" label="set a compartment as the system boundary. All metabolites in this compartment will have the attribute `boundaryCondition` set to true in the sbml." name="boundaryCompartment" optional="true" type="text" value="">
      <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"/>
    <param argument="-ign" checked="false" falsevalue="" label="skip lines with parsing errors instead of stopping the process" name="keepGoing" truevalue="-ign" type="boolean" value="false"/>
  </inputs>
  <outputs>
    <data format="sbml" name="sbml"/>
  </outputs>
  <tests/>
  <help><![CDATA[Create a Sbml File from a tabulated file that contains the reaction ids and the formulas
@ATTRIBUTION@]]></help>
  <citations/>
</tool>