view tools/bigg/GetModelProteome/GetModelProteome.xml @ 5:35c9abcd8934 draft

planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 8577c4cd3ad279c5e97f48f822e041c6b0d90598
author metexplore
date Thu, 12 Jan 2023 13:45:13 +0000
parents ae4c301919c4
children 7a6f2380fc1d
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<?xml version="1.0" encoding="UTF-8"?>
<tool id="met4j_GetModelProteome" name="GetModelProteome" version="1.2.1">
  <description>Get proteome in fasta format of a model present in BIGG</description>
  <xrefs>
    <xref type="bio.tools">met4j</xref>
  </xrefs>
  <requirements>
    <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.2.1</container>
  </requirements>
  <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh bigg.GetModelProteome -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 BIGG]]></help>
  <citations/>
</tool>