<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<tool id="met4j_IdMapper" name="IdMapper" version="@TOOL_VERSION@">
  <description>Map external metabolite identifiers (kegg, metanetx, pubchem CID...) to metabolite ids from a SBML file</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="bio_tools"/>
  <expand macro="requirements"/>
  <command detect_errors="exit_code"><![CDATA[met4j mapping.IdMapper -i "$sbmlPath"
 -id "$inputPath"
 -db "$db"
 $na
 -o "$outputPath"
]]></command>
  <inputs>
    <param argument="-i" format="sbml" label="input SBML file" name="sbmlPath" optional="false" type="data" value=""/>
    <param argument="-id" format="tsv" label="input external id file (one per line)" name="inputPath" optional="false" type="data" value=""/>
    <param argument="-db" label="name of the referenced database annotations to map against, as listed in identifiers.org base uri" name="db" optional="false" type="text" value="">
      <sanitizer invalid_char="_">
        <valid initial="string.printable"/>
      </sanitizer>
    </param>
    <param argument="-na" checked="false" falsevalue="" label="Output id without matching annotation in model, with NA value" name="na" truevalue="-na" type="boolean" value="false"/>
  </inputs>
  <outputs>
    <data format="tsv" name="outputPath"/>
  </outputs>
  <tests/>
  <help><![CDATA[Map external metabolite identifiers (kegg, metanetx, pubchem CID...) to metabolite ids from a SBML file.
The SBML file is expected to contain annotations in MIRIAM format for the selected database:
i.e, <species> entries in the sbml should contain an <annotation> field where there is references to the given database.check identifiers.org for valid database names and associated base URIs.
The input id file should contain one id per line. The output is a tab delimited file with two columns: query id, sbml metabolite id (one line per match)
@ATTRIBUTION@]]></help>
  <citations/>
</tool>