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comparison tools/bigg/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
parents 6a112eaf8f38
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10:6a112eaf8f38 11:40c15b7467f1
1 <?xml version="1.0" encoding="UTF-8" standalone="no"?> 1 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
2 <tool id="met4j_GetBiggModelProteome" name="GetBiggModelProteome" version="2.0.0"> 2 <tool id="met4j_GetBiggModelProteome" name="GetBiggModelProteome" version="2.0.1">
3 <description>Get proteome in fasta format of a model present in the BIGG database</description> 3 <description>Get proteome in fasta format of a model present in the BIGG database</description>
4 <xrefs> 4 <xrefs>
5 <xref type="bio.tools">met4j</xref> 5 <xref type="bio.tools">met4j</xref>
6 </xrefs> 6 </xrefs>
7 <requirements> 7 <requirements>
8 <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0</container> 8 <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.1</container>
9 </requirements> 9 </requirements>
10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh bigg.GetBiggModelProteome -m "$modelId" 10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh bigg.GetBiggModelProteome -m "$modelId"
11 -o "$outputFile" 11 -o "$outputFile"
12 ]]></command> 12 ]]></command>
13 <inputs> 13 <inputs>
20 <outputs> 20 <outputs>
21 <data format="fasta" name="outputFile"/> 21 <data format="fasta" name="outputFile"/>
22 </outputs> 22 </outputs>
23 <tests> 23 <tests>
24 <test maxseconds="120"> 24 <test maxseconds="120">
25
25 <param name="modelId" value="e_coli_core"/> 26 <param name="modelId" value="e_coli_core"/>
27
26 <output ftype="fasta" name="outputFile"> 28 <output ftype="fasta" name="outputFile">
29
27 <assert_contents> 30 <assert_contents>
31
28 <has_line_matching expression=".*name=.*" n="136"/> 32 <has_line_matching expression=".*name=.*" n="136"/>
33
29 </assert_contents> 34 </assert_contents>
35
30 </output> 36 </output>
37
31 </test> 38 </test>
32 </tests> 39 </tests>
33 <help><![CDATA[Get proteome in fasta format of a model present in the BIGG database]]></help> 40 <help><![CDATA[Get proteome in fasta format of a model present in the BIGG database]]></help>
34 <citations> 41 <citations>
35 <citation type="doi">10.1093/nar/gkv1049</citation> 42 <citation type="doi">10.1093/nar/gkv1049</citation>