# 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
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+ `_ 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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diff -r 000000000000 -r 0a5c91d87e46 test-data/uniprod_ids_out.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/uniprod_ids_out.csv Wed Jun 29 09:20:36 2022 +0000
@@ -0,0 +1,1486 @@
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diff -r 000000000000 -r 0a5c91d87e46 test-data/uniprod_ids_out.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/uniprod_ids_out.xml Wed Jun 29 09:20:36 2022 +0000
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