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comparison build/tools/GetModelProteome/GetModelProteome.xml @ 6:7a6f2380fc1d draft

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planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
author metexplore
date Wed, 17 May 2023 13:26:37 +0000
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children 1436e9cde9c9
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5:35c9abcd8934 6:7a6f2380fc1d
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>