Mercurial > repos > metexplore > met4j
diff build/tools/GetGenesFromReactions/GetGenesFromReactions.xml @ 10:6a112eaf8f38 draft
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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--- a/build/tools/GetGenesFromReactions/GetGenesFromReactions.xml Fri Jan 31 18:28:53 2025 +0000 +++ b/build/tools/GetGenesFromReactions/GetGenesFromReactions.xml Mon Feb 03 15:59:46 2025 +0000 @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8" standalone="no"?> -<tool id="met4j_GetGenesFromReactions" name="GetGenesFromReactions" version="develop"> +<tool id="met4j_GetGenesFromReactions" name="GetGenesFromReactions" version="2.0.0"> <description>Get gene lists from a list of reactions and a SBML file.</description> <xrefs> <xref type="bio.tools">met4j</xref> </xrefs> <requirements> - <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.GetGenesFromReactions -i "$sbml" -r "$reactionFile" @@ -34,125 +34,15 @@ </outputs> <tests> <test> - - - - - - - - - - - <param name="sbml" value="XF_network.sbml"/> - - - - - - - - - - - <param name="reactionFile" value="XF_network_R_Seed.tab"/> - - - - - - - - - - - <output ftype="tsv" name="outputFile"> - - - - - - - - - - - <assert_contents> - - - - - - - - - - - <has_n_lines n="2"/> - - - - - - - - - - - <has_line_matching expression="R_GLUN.*XFCFBP8418_026750" n="1"/> - - - - - - - - - - - <has_line_matching expression="R_ACGS.*XFCFBP8418_025260" n="1"/> - - - - - - - - - - - </assert_contents> - - - - - - - - - - - </output> - - - - - - - - - - - </test> </tests> <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>