# HG changeset patch # User iuc # Date 1656494436 0 # Node ID 0a5c91d87e46b4399483667324ce0a86c60a5882 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/selenzy_wrapper commit ae90bec837703e870850cbeced41aa691869455f diff -r 000000000000 -r 0a5c91d87e46 selenzy_wrapper.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/selenzy_wrapper.xml Wed Jun 29 09:20:36 2022 +0000 @@ -0,0 +1,97 @@ + + Performs enzyme selection from a reaction query + + 0 + 0.3.0 + + + selenzy_wrapper + + + + +
+ + + + + + +
+
+ + + + + + + + + + + + + `_ and outputs an updated SBML file annotated with the enzyme UniProt IDs, as well as in CSV format. + +Input +----- + +* **Pathway (SBML)**\ : SBML pathway file +* **Number of targets to display in results**\ : (integer) Number of targets to display in results (before taxon IDs filtering) [default = 500] +* **Number of uniprot IDs with top score to keep**\ : (integer) Number of enzyme IDs to display in results (after taxon IDs filtering) [default = -1 (no limit)] +* **Use similarity values for preferred reaction direction only**\ : (float) Use similarity values for preferred reaction direction only [default=0 (OFF)] +* **Do not compute MSA/conservation scores ?**\ : (boolean) Do not compute Multiple Sequence Alignment and conservation scores ? (MSA scores are computed by default) +* **Host taxon ID**\ : (string) Taxon ID of the chassis (default: 83333 [E. coli K12]) +* **Comma separated taxon IDs of output enzyme sequences**\ : (string) Comma separated taxon IDs of output enzyme sequences + +Output +------ + +* **Uniprot IDs (SBML)**\ : Annotated SBML pathway. +* **Uniprot IDs (CSV)**\ : Annotated CSV pathway. + +Project Links +------------------ + +* `GitHub `_ + +Version +---------- + +0.3.0 + +Authors +------- +* **Joan Hérisson** + +License +------- + +* `MIT `_ + +Acknowledgments +--------------- + +* Thomas Duigou + + ]]> + + 10.1093/bioinformatics/bty065 + +
\ No newline at end of file diff -r 000000000000 -r 0a5c91d87e46 test-data/pathway.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/pathway.xml Wed Jun 29 09:20:36 2022 +0000 @@ -0,0 +1,626 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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