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annotate tools/bigg/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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1 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
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2 <tool id="met4j_GetBiggModelProteome" name="GetBiggModelProteome" version="develop">
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3 <description>Get proteome in fasta format of a model present in the BIGG database</description>
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4 <xrefs>
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5 <xref type="bio.tools">met4j</xref>
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6 </xrefs>
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7 <requirements>
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8 <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop</container>
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9 </requirements>
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10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh bigg.GetBiggModelProteome -m "$modelId"
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11 -o "$outputFile"
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12 ]]></command>
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13 <inputs>
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14 <param argument="-m" label="[ex: iMM904] id of the BIGG model" name="modelId" optional="false" type="text" value="iMM904">
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15 <sanitizer invalid_char="_">
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16 <valid initial="string.printable"/>
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17 </sanitizer>
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18 </param>
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19 </inputs>
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20 <outputs>
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21 <data format="fasta" name="outputFile"/>
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22 </outputs>
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23 <tests>
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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>
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74 </tests>
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75 <help><![CDATA[Get proteome in fasta format of a model present in the BIGG database]]></help>
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76 <citations>
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77 <citation type="doi">10.1093/nar/gkv1049</citation>
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78 </citations>
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79 </tool>