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comparison build/tools/GetGenesFromReactions/GetGenesFromReactions.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
parents 1274e2a62479
children 6a112eaf8f38
comparison
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8:1274e2a62479 9:0976a6257300
1 <?xml version="1.0" encoding="UTF-8"?> 1 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
2 <tool id="met4j_GetGenesFromReactions" name="GetGenesFromReactions" version="1.5.0"> 2 <tool id="met4j_GetGenesFromReactions" name="GetGenesFromReactions" version="develop">
3 <description>Get gene lists from a list of reactions and a GSMN.</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:1.5.0</container> 8 <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop</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 <param name="sbml" value="XF_network.sbml"/> 37
38 <param name="reactionFile" value="XF_network_R_Seed.tab"/> 38
39 <output ftype="tsv" name="outputFile"> 39
40 <assert_contents> 40
41 <has_n_lines n="2"/> 41
42 <has_line_matching expression="R_GLUN.*XFCFBP8418_026750" n="1"/> 42
43 <has_line_matching expression="R_ACGS.*XFCFBP8418_025260" n="1"/> 43
44 </assert_contents> 44
45 </output> 45
46 </test> 46
47
48 <param name="sbml" value="XF_network.sbml"/>
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60 <param name="reactionFile" value="XF_network_R_Seed.tab"/>
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72 <output ftype="tsv" name="outputFile">
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84 <assert_contents>
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96 <has_n_lines n="2"/>
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108 <has_line_matching expression="R_GLUN.*XFCFBP8418_026750" n="1"/>
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120 <has_line_matching expression="R_ACGS.*XFCFBP8418_025260" n="1"/>
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132 </assert_contents>
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144 </output>
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156 </test>
47 </tests> 157 </tests>
48 <help><![CDATA[Get associated gene list from a list of reactions and a GSMN. Parse GSMN 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> 158 <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/> 159 <citations/>
50 </tool> 160 </tool>