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comparison build/tools/GetBiggModelProteome/GetBiggModelProteome.xml @ 9:0976a6257300 draft

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planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 05db35f63cadb9d56dafff594a3507c59cd85273
author metexplore
date Fri, 31 Jan 2025 18:28:53 +0000
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8:1274e2a62479 9:0976a6257300
1 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
2 <tool id="met4j_GetBiggModelProteome" name="GetBiggModelProteome" version="develop">
3 <description>Get proteome in fasta format of a model present in the BIGG database</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:develop</container>
9 </requirements>
10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh bigg.GetBiggModelProteome -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">
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31 <param name="modelId" value="e_coli_core"/>
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38 <output ftype="fasta" name="outputFile">
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45 <assert_contents>
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52 <has_line_matching expression=".*name=.*" n="136"/>
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59 </assert_contents>
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66 </output>
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73 </test>
74 </tests>
75 <help><![CDATA[Get proteome in fasta format of a model present in the BIGG database]]></help>
76 <citations>
77 <citation type="doi">10.1093/nar/gkv1049</citation>
78 </citations>
79 </tool>