Mercurial > repos > metexplore > met4j
comparison build/tools/GetModelProteome/GetModelProteome.xml @ 6:7a6f2380fc1d draft
planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
author | metexplore |
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date | Wed, 17 May 2023 13:26:37 +0000 |
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children | 1436e9cde9c9 |
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5:35c9abcd8934 | 6:7a6f2380fc1d |
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1 <?xml version="1.0" encoding="UTF-8"?> | |
2 <tool id="met4j_GetModelProteome" name="GetModelProteome" version="1.3.0"> | |
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:1.3.0</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 <citations/> | |
35 </tool> |