annotate tools/convert/Kegg2Sbml/Kegg2Sbml.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_Kegg2Sbml" name="Kegg2Sbml" version="0.11.0">
  <description>Build a SBML file from KEGG organism-specific pathways. Uses Kegg API.</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 convert.Kegg2Sbml#if str($org):
 -org "$org"
#end if
 -sbml "$sbml"
]]></command>
  <inputs>
    <param argument="-org" label="[] Kegg org id. Must be 3 letters (" name="org" optional="true" type="text" value="">
      <sanitizer invalid_char="_">
        <valid initial="string.printable"/>
      </sanitizer>
    </param>
  </inputs>
  <outputs>
    <data format="sbml" name="sbml"/>
  </outputs>
  <tests>
    <test maxseconds="600">
      <param name="org" value="buc"/>
      <output ftype="sbml" name="sbml">
        <assert_contents>
          <is_valid_xml/>

        </assert_contents>
      </output>
    </test>
  </tests>
  <help><![CDATA[Build a SBML file from KEGG organism-specific pathways. Uses Kegg API.
Errors returned by this program could be due to Kegg API dysfunctions or limitations. Try later if this problem occurs.]]></help>
</tool>