# HG changeset patch
# User nml
# Date 1557425794 14400
# Node ID deebc6410d13b973455f8e0821ab8e1e0d58d095
# Parent  8529045f0fdfb011e84ab5201563147e073e7c67
planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit bbf7dd6b56e8ee77cff1f98a42a5abadd681b7ac

diff -r 8529045f0fdf -r deebc6410d13 mykrobe_parser.R
--- a/mykrobe_parser.R	Thu Apr 25 10:13:46 2019 -0400
+++ b/mykrobe_parser.R	Thu May 09 14:16:34 2019 -0400
@@ -291,7 +291,7 @@
         mutate(variants = strsplit(variants, "__")) %>% # Split the mutations across rows (list first then split across rows)
         unnest(variants) %>% 
         separate(variants, c("gene", "mutation"), "_") %>% 
-        mutate(columnname = ifelse(gene %in% c("tlyA", "rrs", "eis", "gid"), # Check for columns that include the drug name or not and paste accordingly
+        mutate(columnname = ifelse(gene %in% c("gyrA", "tlyA", "rrs", "eis", "gid"), # Check for columns that include the drug name or not and paste accordingly
                                    paste("Mykrobe", drug, gene, sep = "_"),
                                    paste("Mykrobe", gene, sep = "_"))) %>% 
         # Extract out the mutation information with a regex that covers all potential genes
diff -r 8529045f0fdf -r deebc6410d13 mykrobe_parser.xml
--- a/mykrobe_parser.xml	Thu Apr 25 10:13:46 2019 -0400
+++ b/mykrobe_parser.xml	Thu May 09 14:16:34 2019 -0400
@@ -1,4 +1,4 @@
-<tool id="mykrobe_parseR" name="mykrobe_parseR" version="0.1.4">
+<tool id="mykrobe_parseR" name="mykrobe_parseR" version="0.1.4.1">
     <requirements>
         <requirement type="package" version="3.4.1">r-base</requirement>
         <requirement type="package" version="1.5.0">r-jsonlite</requirement>