annotate tools/attributes/SbmlToMetaboliteTable/SbmlToMetaboliteTable.xml @ 0:3cdcfdae8bd2 draft default tip

"planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit a58b6f8a6dde6ef64da64ee50395dc5bc848167a-dirty"

<?xml version="1.0" encoding="UTF-8"?>
<tool id="met4j_SbmlToMetaboliteTable" name="SbmlToMetaboliteTable" version="0.11.0">
  <description>Create a tabulated file with metabolite attributes from a SBML file</description>
  <xrefs>
    <xref type="bio.tools">met4j</xref>
  </xrefs>
  <requirements>
    <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:0.11.0</container>
  </requirements>
  <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.SbmlToMetaboliteTable -s "$sbml"
 -o "$outputFile"
]]></command>
  <inputs>
    <param argument="-s" format="sbml" label="Sbml file" name="sbml" optional="false" type="data" value=""/>
  </inputs>
  <outputs>
    <data format="tsv" name="outputFile"/>
  </outputs>
  <tests>
    <test>
      <param name="sbml" value="toy_model.xml"/>
      <output ftype="tsv" name="outputFile">
        <assert_contents>
          <has_n_lines n="9"/>
          <has_n_columns n="6"/>
          <has_line_matching expression=".*1S/C2H6O/c1-2-3/h3H,2H2,1H3.*" n="1"/>
          <has_line_matching expression=".*C.*NC.*" n="1"/>
        </assert_contents>
      </output>
    </test>
  </tests>
  <help><![CDATA[Create a tabulated file with metabolite attributes from a SBML file]]></help>
</tool>