annotate MassMapper.xml @ 0:4928b239a36d draft

planemo upload for repository https://forge.inrae.fr/metexplore/met4j-galaxy commit 71335d4a636672d264cc4f443c07856907571928

<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<tool id="met4j_MassMapper" name="MassMapper" version="@TOOL_VERSION@">
  <description>Retrieve metabolites in a SBML file from their mass.</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="bio_tools"/>
  <expand macro="requirements"/>
  <command detect_errors="exit_code"><![CDATA[met4j mapping.MassMapper -i "$sbmlPath"
 -m "$inputPath"
#if str($ppm) != 'nan':
 -ppm "$ppm"
#end if
 $na
#if str($compute):
 -comp "$compute"
#end if
 -o "$outputPath"
]]></command>
  <inputs>
    <param argument="-i" format="sbml" label="input SBML file" name="sbmlPath" optional="false" type="data" value=""/>
    <param argument="-m" format="tsv" label="input mass file (one per line)" name="inputPath" optional="false" type="data" value=""/>
    <param argument="-ppm" label="mass delta tolerance in part per million" name="ppm" optional="true" type="float" value="5.0"/>
    <param argument="-na" checked="false" falsevalue="" label="Output mass without match in model, with NA value" name="na" truevalue="-na" type="boolean" value="false"/>
    <param argument="-comp" label="Method for computing mass from formulas" name="compute" optional="true" type="select" value="average">
      <option selected="true" value="average">average</option>
      <option value="monoisotopic">monoisotopic</option>
    </param>
  </inputs>
  <outputs>
    <data format="tsv" name="outputPath"/>
  </outputs>
  <tests/>
  <help><![CDATA[Retrieve metabolites in a SBML file from their mass.
The SBML file is expected to contain fbc:chemicalFormula attributes for species entries, in order to compute masses.
The input mass file should contain one mass per line. The output is a tab delimited file with two columns: query mass, sbml metabolite id (one line per match)
@ATTRIBUTION@]]></help>
  <citations/>
</tool>