Mercurial > repos > metexplore > met4j
diff tools/attributes/GetReactantsFromReactions/GetReactantsFromReactions.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 |
line wrap: on
line diff
--- a/tools/attributes/GetReactantsFromReactions/GetReactantsFromReactions.xml Fri Jan 31 18:28:53 2025 +0000 +++ b/tools/attributes/GetReactantsFromReactions/GetReactantsFromReactions.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_GetReactantsFromReactions" name="GetReactantsFromReactions" version="develop"> +<tool id="met4j_GetReactantsFromReactions" name="GetReactantsFromReactions" version="2.0.0"> <description>Get reactant 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.GetReactantsFromReactions -i "$sbml" -r "$reactionFile" @@ -38,355 +38,36 @@ </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_text_matching expression="R_GLUN" n="4"/> - - - - - - - - - - - <has_text_matching expression="R_ACGS" n="5"/> - - - - - - - - - - - </assert_contents> - - - - - - - - - - - </output> - - - - - - - - - - - </test> <test> - - - - - - - - - - - <param name="sbml" value="XF_network.sbml"/> - - - - - - - - - - - <param name="reactionFile" value="XF_network_R_Seed.tab"/> - - - - - - - - - - - <param name="printSubstrates" value="true"/> - - - - - - - - - - - <output ftype="tsv" name="outputFile"> - - - - - - - - - - - <assert_contents> - - - - - - - - - - - <has_text_matching expression="R_GLUN" n="2"/> - - - - - - - - - - - <has_text_matching expression="R_ACGS" n="5"/> - - - - - - - - - - - </assert_contents> - - - - - - - - - - - </output> - - - - - - - - - - - </test> <test> - - - - - - - - - - - <param name="sbml" value="XF_network.sbml"/> - - - - - - - - - - - <param name="reactionFile" value="XF_network_R_Seed.tab"/> - - - - - - - - - - - <param name="printProducts" value="true"/> - - - - - - - - - - - <output ftype="tsv" name="outputFile"> - - - - - - - - - - - <assert_contents> - - - - - - - - - - - <has_text_matching expression="R_GLUN" n="2"/> - - - - - - - - - - - <has_text_matching expression="R_ACGS" n="5"/> - - - - - - - - - - - </assert_contents> - - - - - - - - - - - </output> - - - - - - - - - - - </test> </tests> <help><![CDATA[Get reactant lists from a list of reactions and a Sbml file. Output a tab-separated file with one row per reactant, reaction identifiers in first column, reactant identifiers in second column. It can provides substrates, products, or both (by default). In the case of reversible reactions, all reactants are considered as both substrates and products]]></help>