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annotate build/tools/GetBiggModelProteome/GetBiggModelProteome.xml @ 11:40c15b7467f1 draft default tip

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planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 61dbdbae896d18b519a470e056cb8b4f98394518
author metexplore
date Thu, 13 Feb 2025 15:08:22 +0000
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0976a6257300 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 05db35f63cadb9d56dafff594a3507c59cd85273
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1 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
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2 <tool id="met4j_GetBiggModelProteome" name="GetBiggModelProteome" version="2.0.1">
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3 <description>Get proteome in fasta format of a model present in the BIGG database</description>
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4 <xrefs>
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5 <xref type="bio.tools">met4j</xref>
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6 </xrefs>
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7 <requirements>
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8 <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.1</container>
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9 </requirements>
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10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh bigg.GetBiggModelProteome -m "$modelId"
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11 -o "$outputFile"
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12 ]]></command>
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13 <inputs>
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14 <param argument="-m" label="[ex: iMM904] id of the BIGG model" name="modelId" optional="false" type="text" value="iMM904">
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15 <sanitizer invalid_char="_">
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16 <valid initial="string.printable"/>
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17 </sanitizer>
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18 </param>
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19 </inputs>
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20 <outputs>
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21 <data format="fasta" name="outputFile"/>
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22 </outputs>
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23 <tests>
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24 <test maxseconds="120">
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26 <param name="modelId" value="e_coli_core"/>
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28 <output ftype="fasta" name="outputFile">
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30 <assert_contents>
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32 <has_line_matching expression=".*name=.*" n="136"/>
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34 </assert_contents>
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36 </output>
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38 </test>
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39 </tests>
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40 <help><![CDATA[Get proteome in fasta format of a model present in the BIGG database]]></help>
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41 <citations>
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42 <citation type="doi">10.1093/nar/gkv1049</citation>
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43 </citations>
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44 </tool>