view GetBiggModelProteome.xml @ 2:ddc8160220b9 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_GetBiggModelProteome" name="GetBiggModelProteome" version="@TOOL_VERSION@">
  <description>Get proteome in fasta format of a model present in the BIGG database</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="bio_tools"/>
  <expand macro="requirements"/>
  <command detect_errors="exit_code"><![CDATA[met4j bigg.GetBiggModelProteome -m "$modelId"
 -o "$outputFile"
]]></command>
  <inputs>
    <param argument="-m" label="[ex: iMM904] id of the BIGG model" name="modelId" optional="false" type="text" value="iMM904">
      <sanitizer invalid_char="_">
        <valid initial="string.printable"/>
      </sanitizer>
    </param>
  </inputs>
  <outputs>
    <data format="fasta" name="outputFile"/>
  </outputs>
  <tests>
    <test maxseconds="120">
      <param name="modelId" value="e_coli_core"/>
      <output ftype="fasta" name="outputFile">
        <assert_contents>
          <has_line_matching expression=".*name=.*" n="136"/>
        </assert_contents>
      </output>
    </test>
  </tests>
  <help><![CDATA[Get proteome in fasta format of a model present in the BIGG database
@ATTRIBUTION@]]></help>
  <citations>
    <citation type="doi">10.1093/nar/gkv1049</citation>
  </citations>
</tool>