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comparison build/tools/GetBiggModelProteome/GetBiggModelProteome.xml @ 10:6a112eaf8f38 draft

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planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 71071300dd662ad01bd064abcf6866a192eeea95
author metexplore
date Mon, 03 Feb 2025 15:59:46 +0000
parents 0976a6257300
children 40c15b7467f1
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9:0976a6257300 10:6a112eaf8f38
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="develop"> 2 <tool id="met4j_GetBiggModelProteome" name="GetBiggModelProteome" version="2.0.0">
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:develop</container> 8 <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0</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">
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31 <param name="modelId" value="e_coli_core"/> 25 <param name="modelId" value="e_coli_core"/>
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38 <output ftype="fasta" name="outputFile"> 26 <output ftype="fasta" name="outputFile">
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45 <assert_contents> 27 <assert_contents>
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52 <has_line_matching expression=".*name=.*" n="136"/> 28 <has_line_matching expression=".*name=.*" n="136"/>
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59 </assert_contents> 29 </assert_contents>
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66 </output> 30 </output>
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73 </test> 31 </test>
74 </tests> 32 </tests>
75 <help><![CDATA[Get proteome in fasta format of a model present in the BIGG database]]></help> 33 <help><![CDATA[Get proteome in fasta format of a model present in the BIGG database]]></help>
76 <citations> 34 <citations>
77 <citation type="doi">10.1093/nar/gkv1049</citation> 35 <citation type="doi">10.1093/nar/gkv1049</citation>