Mercurial > repos > metexplore > met4j
diff tools/attributes/SetIds/SetIds.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/tools/attributes/SetIds/SetIds.xml Fri Jan 31 18:28:53 2025 +0000 +++ b/tools/attributes/SetIds/SetIds.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_SetIds" name="SetIds" version="develop"> +<tool id="met4j_SetIds" name="SetIds" version="2.0.0"> <description>Set new ids to network objects in a SBML file from a tabulated file containing the old ids and the new ids</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.SetIds#if str($colname) != 'nan': -cnew "$colname" @@ -62,387 +62,63 @@ </outputs> <tests> <test> - - - - - - <param name="sbml" value="toy_model.xml"/> - - - - - - <param name="tab" value="idMetabolites.tsv"/> - - - - - - <param name="o" value="METABOLITE"/> - - - - - - <output ftype="sbml" name="out"> - - - - - - <assert_contents> - - - - - - <is_valid_xml/> - - - - - - <has_line_matching expression=".*id=.metaboliteA.*" n="1"/> - - - - - - <has_line_matching expression=".*id=.metaboliteB.*" n="1"/> - - - - - - </assert_contents> - - - - - - </output> - - - - - - </test> <test> - - - - - - <param name="sbml" value="toy_model.xml"/> - - - - - - <param name="tab" value="idReactions.tsv"/> - - - - - - <output ftype="sbml" name="out"> - - - - - - <assert_contents> - - - - - - <is_valid_xml/> - - - - - - <has_line_matching expression=".*id=.reaction1.*" n="1"/> - - - - - - <has_line_matching expression=".*id=.reaction2.*" n="1"/> - - - - - - </assert_contents> - - - - - - </output> - - - - - - </test> <test> - - - - - - <param name="sbml" value="XF_network.sbml"/> - - - - - - <param name="tab" value="idPathways.tsv"/> - - - - - - <param name="o" value="PATHWAY"/> - - - - - - <output ftype="sbml" name="out"> - - - - - - <assert_contents> - - - - - - <is_valid_xml/> - - - - - - <has_line_matching expression=".*groups:id=.CEB.*" n="1"/> - - - - - - <has_line_matching expression=".*groups:id=.NSP.*" n="1"/> - - - - - - </assert_contents> - - - - - - </output> - - - - - - </test> <test> - - - - - - <param name="sbml" value="XF_network.sbml"/> - - - - - - <param name="tab" value="idGenes.tsv"/> - - - - - - <param name="o" value="GENE"/> - - - - - - <output ftype="sbml" name="out"> - - - - - - <assert_contents> - - - - - - <is_valid_xml/> - - - - - - <has_line_matching expression=".*fbc:id=.G1.*" n="1"/> - - - - - - <has_line_matching expression=".*fbc:id=.G2.*" n="1"/> - - - - - - </assert_contents> - - - - - - </output> - - - - - - </test> <test> - - - - - - <param name="sbml" value="XF_network.sbml"/> - - - - - - <param name="tab" value="idCompartments.tsv"/> - - - - - - <param name="o" value="COMPARTMENT"/> - - - - - - <output ftype="sbml" name="out"> - - - - - - <assert_contents> - - - - - - <is_valid_xml/> - - - - - - <has_line_matching expression=".*id=.cytosol.*" n="1"/> - - - - - - <has_line_matching expression=".*id=.extra.*" n="1"/> - - - - - - </assert_contents> - - - - - - </output> - - - - - - </test> </tests> <help><![CDATA[Set new ids to network objects in a SBML file from a tabulated file containing the old ids and the new ids