annotate FbcToNotes.xml @ 1:a7a87049909a draft

planemo upload for repository https://forge.inrae.fr/metexplore/met4j-galaxy commit 6bb33ff0ff022029543e5e5ace7d16418715aa1c

<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<tool id="met4j_FbcToNotes" name="FbcToNotes" version="@TOOL_VERSION@">
  <description>Convert FBC package annotations to sbml html notes</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="bio_tools"/>
  <expand macro="requirements"/>
  <command detect_errors="exit_code"><![CDATA[met4j convert.FbcToNotes -i "$inputPath"
 -o "$outputPath"
]]></command>
  <inputs>
    <param argument="-i" format="sbml" label="input SBML file" name="inputPath" optional="false" type="data" value=""/>
  </inputs>
  <outputs>
    <data format="sbml" name="outputPath"/>
  </outputs>
  <tests>
    <test>
      <param name="inputPath" value="ECOL.xml"/>
      <output ftype="sbml" name="outputPath">
        <assert_contents>
          <is_valid_xml/>
          <has_line_matching expression=".*GENE_ASSOCIATION: b2312.*" n="1"/>
        </assert_contents>
      </output>
    </test>
  </tests>
  <help><![CDATA[Convert FBC package annotations to sbml html notes
Convert FBC package annotations to sbml html notes.Be careful, the app reads only fbc annotations, the existing html notes will be overwritten.
@ATTRIBUTION@]]></help>
  <citations>
    <citation type="doi">10.1515/jib-2017-0082</citation>
  </citations>
</tool>