Mercurial > repos > nml > mykrobe_parser
changeset 5:deebc6410d13 draft
planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit bbf7dd6b56e8ee77cff1f98a42a5abadd681b7ac
| author | nml |
|---|---|
| date | Thu, 09 May 2019 14:16:34 -0400 |
| parents | 8529045f0fdf |
| children | 8e7e5a660942 |
| files | mykrobe_parser.R mykrobe_parser.xml |
| diffstat | 2 files changed, 2 insertions(+), 2 deletions(-) [+] |
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--- 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
--- 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>