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comparison tools/attributes/GetGenesFromReactions/GetGenesFromReactions.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_GetGenesFromReactions" name="GetGenesFromReactions" version="2.0.0"> 2 <tool id="met4j_GetGenesFromReactions" name="GetGenesFromReactions" version="2.0.1">
3 <description>Get gene lists from a list of reactions and a SBML file.</description> 3 <description>Get gene lists from a list of reactions and a SBML file.</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 attributes.GetGenesFromReactions -i "$sbml" 10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.GetGenesFromReactions -i "$sbml"
11 -r "$reactionFile" 11 -r "$reactionFile"
12 #if str($sep): 12 #if str($sep):
13 -sep "$sep" 13 -sep "$sep"
32 <outputs> 32 <outputs>
33 <data format="tsv" name="outputFile"/> 33 <data format="tsv" name="outputFile"/>
34 </outputs> 34 </outputs>
35 <tests> 35 <tests>
36 <test> 36 <test>
37
37 <param name="sbml" value="XF_network.sbml"/> 38 <param name="sbml" value="XF_network.sbml"/>
39
38 <param name="reactionFile" value="XF_network_R_Seed.tab"/> 40 <param name="reactionFile" value="XF_network_R_Seed.tab"/>
41
39 <output ftype="tsv" name="outputFile"> 42 <output ftype="tsv" name="outputFile">
43
40 <assert_contents> 44 <assert_contents>
45
41 <has_n_lines n="2"/> 46 <has_n_lines n="2"/>
47
42 <has_line_matching expression="R_GLUN.*XFCFBP8418_026750" n="1"/> 48 <has_line_matching expression="R_GLUN.*XFCFBP8418_026750" n="1"/>
49
43 <has_line_matching expression="R_ACGS.*XFCFBP8418_025260" n="1"/> 50 <has_line_matching expression="R_ACGS.*XFCFBP8418_025260" n="1"/>
51
44 </assert_contents> 52 </assert_contents>
53
45 </output> 54 </output>
55
46 </test> 56 </test>
47 </tests> 57 </tests>
48 <help><![CDATA[Get associated gene list from a list of reactions and a SBML file. Parse SBML GPR annotations and output a tab-separated file with one row per gene, associated reaction identifiers from input file in first column, gene identifiers in second column.]]></help> 58 <help><![CDATA[Get associated gene list from a list of reactions and a SBML file. Parse SBML GPR annotations and output a tab-separated file with one row per gene, associated reaction identifiers from input file in first column, gene identifiers in second column.]]></help>
49 <citations/> 59 <citations/>
50 </tool> 60 </tool>