annotate FormulaMapper.xml @ 1:927af2eb6534 draft default tip

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_FormulaMapper" name="FormulaMapper" version="@TOOL_VERSION@">
  <description>Retrieve metabolites in a SBML file from their chemical formula</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="bio_tools"/>
  <expand macro="requirements"/>
  <command detect_errors="exit_code"><![CDATA[met4j mapping.FormulaMapper -i "$sbmlPath"
 -f "$inputPath"
 $na
 -o "$outputPath"
]]></command>
  <inputs>
    <param argument="-i" format="sbml" label="input SBML file" name="sbmlPath" optional="false" type="data" value=""/>
    <param argument="-f" format="tsv" label="input formula file (one per line)" name="inputPath" optional="false" type="data" value=""/>
    <param argument="-na" checked="false" falsevalue="" label="Output formulas without match in model, with NA value" name="na" truevalue="-na" type="boolean" value="false"/>
  </inputs>
  <outputs>
    <data format="tsv" name="outputPath"/>
  </outputs>
  <tests/>
  <help><![CDATA[Retrieve metabolites in a SBML file from their chemical formula. 
The SBML file is expected to contain fbc:chemicalFormula attributes for species entries.
The input formula file should contain one formula per line. The output is a tab delimited file with two columns: query formula, sbml metabolite id (one line per match)
@ATTRIBUTION@]]></help>
  <citations/>
</tool>