Mercurial > repos > metexplore > met4j
comparison tools/bigg/GetModelProteome/GetModelProteome.xml @ 0:dcd16521b969 draft
planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 5dab0a2d83a1fdd7a1878a50ba0f24e752505393
| author | metexplore |
|---|---|
| date | Fri, 10 Jun 2022 10:31:34 +0000 |
| parents | |
| children | 9b162ee6ff8e |
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| -1:000000000000 | 0:dcd16521b969 |
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| 1 <?xml version="1.0" encoding="UTF-8"?> | |
| 2 <tool id="met4j_GetModelProteome" name="GetModelProteome" version="0.11.0"> | |
| 3 <description>Get proteome in fasta format of a model present in BIGG</description> | |
| 4 <xrefs> | |
| 5 <xref type="bio.tools">met4j</xref> | |
| 6 </xrefs> | |
| 7 <requirements> | |
| 8 <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:0.11.0</container> | |
| 9 </requirements> | |
| 10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh bigg.GetModelProteome -m "$modelId" | |
| 11 -o "$outputFile" | |
| 12 ]]></command> | |
| 13 <inputs> | |
| 14 <param argument="-m" label="[ex: iMM904] id of the BIGG model" name="modelId" optional="false" type="text" value="iMM904"> | |
| 15 <sanitizer invalid_char="_"> | |
| 16 <valid initial="string.printable"/> | |
| 17 </sanitizer> | |
| 18 </param> | |
| 19 </inputs> | |
| 20 <outputs> | |
| 21 <data format="fasta" name="outputFile"/> | |
| 22 </outputs> | |
| 23 <tests> | |
| 24 <test maxseconds="120"> | |
| 25 <param name="modelId" value="e_coli_core"/> | |
| 26 <output ftype="fasta" name="outputFile"> | |
| 27 <assert_contents> | |
| 28 <has_line_matching expression=".*name=.*" n="136"/> | |
| 29 </assert_contents> | |
| 30 </output> | |
| 31 </test> | |
| 32 </tests> | |
| 33 <help><![CDATA[Get proteome in fasta format of a model present in BIGG]]></help> | |
| 34 </tool> |