<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<tool id="met4j_SetGprs" name="SetGprs" version="@TOOL_VERSION@">
  <description>Create a new SBML file from an original sbml file and a tabulated file containing reaction ids and Gene association written in a cobra way</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="bio_tools"/>
  <expand macro="requirements"/>
  <command detect_errors="exit_code"><![CDATA[met4j attributes.SetGprs#if str($colgpr) != 'nan':
 -cgpr "$colgpr"
#end if
#if str($colid) != 'nan':
 -ci "$colid"
#end if
 $p
#if str($nSkip):
 -n "$nSkip"
#end if
 -i "$sbml"
#if str($tab) != 'None':
 -tab "$tab"
#end if
#if str($c):
 -c "$c"
#end if
 -o "$out"
]]></command>
  <inputs>
    <param argument="-cgpr" label="[2] number of the column where are the gprs" name="colgpr" optional="true" type="integer" value="2"/>
    <param argument="-ci" label="[1] number of the column where are the reaction 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 R_ to reactions" name="p" truevalue="-p" 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="-i" format="sbml" label="Original SBML file" name="sbml" optional="false" type="data" value=""/>
    <param argument="-tab" format="tsv" label="Input 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/>
  <help><![CDATA[Create a new SBML file from an original sbml file and a tabulated file containing reaction ids and Gene association written in a cobra way
The ids must correspond between the tabulated file and the SBML file.
If prefix R_ is present in the ids in the SBML file and not in the tabulated file, use the -p option.
GPR must be written in a cobra way in the tabulated file as described in Schellenberger et al 2011 Nature Protocols 6(9):1290-307
(The GPR will be written in the SBML file in two locations:
- in the reaction html notes (GENE_ASSOCIATION: ( XC_0401 ) OR ( XC_3282 ))
- as fbc gene product association (see FBC package specifications: https://doi.org/10.1515/jib-2017-0082)
@ATTRIBUTION@]]></help>
  <citations>
    <citation type="doi">10.1515/jib-2017-0082</citation>
    <citation type="doi">10.1038/nprot.2011.308</citation>
  </citations>
</tool>