Mercurial > repos > nml > mykrobe_parser
changeset 4:8529045f0fdf draft
planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 34d9c47b9451e5f7843028dba22b96d125fb09f5
| author | nml |
|---|---|
| date | Thu, 25 Apr 2019 10:13:46 -0400 |
| parents | 0dcfdec76c3c |
| children | deebc6410d13 |
| files | mykrobe_parser.R mykrobe_parser.xml |
| diffstat | 2 files changed, 16 insertions(+), 14 deletions(-) [+] |
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--- a/mykrobe_parser.R Fri Oct 26 16:57:34 2018 -0400 +++ b/mykrobe_parser.R Thu Apr 25 10:13:46 2019 -0400 @@ -152,7 +152,7 @@ opt$depth, # Mykrobe_min_depth_default_5 opt$conf, # Mykrobe_min_conf_default_10 "", # LIMS_file - empty as it's an upload field in LIMS - opt$name) # LIMS_filename + opt$name) # Mutation_set_version names(params) <- c("Lims_Comment", "Lims_INTComment", @@ -160,7 +160,7 @@ "Mykrobe_min_depth_default_5", "Mykrobe_min_conf_default_10", "LIMS_file", - "LIMS_filename") + "Mutation_set_version") # A default report in the order our LIMS requires @@ -185,9 +185,12 @@ "Mykrobe_rpsA", "Pyrazinamide_R_mutations", "Pyrazinamide_Prediction", - "Mykrobe_gyrA", - "Quinolones_R_mutations", - "Quinolones_Prediction", + "Mykrobe_Ofloxacin_gyrA", + "Ofloxacin_R_mutations", + "Ofloxacin_Prediction", + "Mykrobe_Moxifloxacin_gyrA", + "Moxifloxacin_R_mutations", + "Moxifloxacin_Prediction", "Mykrobe_rpsL", "Mykrobe_Streptomycin_rrs", "Mykrobe_Streptomycin_gid", @@ -212,7 +215,7 @@ "Mykrobe_min_depth_default_5", "Mykrobe_min_conf_default_10", "LIMS_file", - "LIMS_filename") + "Mutation_set_version") report <- setNames(data.frame(matrix("", ncol = length(columns), nrow = 1), stringsAsFactors = F), columns) @@ -222,7 +225,8 @@ "Rifampicin", "Ethambutol", "Pyrazinamide", - "Moxifloxacin_Ofloxacin", + "Moxifloxacin", + "Ofloxacin", "Streptomycin", "Amikacin", "Capreomycin", @@ -287,7 +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", "gid"), # Check for columns that include the drug name or not and paste accordingly + mutate(columnname = ifelse(gene %in% c("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 @@ -332,9 +336,7 @@ filter_at(vars(ends_with("_Prediction")), any_vars(. != "failed")) %>% mutate_at(vars(starts_with("Mykrobe_")), funs(replace(., is.na(.), "No Mutation"))) %>% full_join(anti_join(report, ., by = "file")) %>% - select(columns) %>% - rename(Moxifloxacin_Ofloxacin_R_mutations = Quinolones_R_mutations, - Moxifloxacin_Ofloxacin_Prediction = Quinolones_Prediction) + select(columns) # Add in the parameters fed from Galaxy using named character vector @@ -347,7 +349,7 @@ Mykrobe_min_depth_default_5 = params["Mykrobe_min_depth_default_5"], Mykrobe_min_conf_default_10 = params["Mykrobe_min_conf_default_10"], LIMS_file = params["LIMS_file"], - LIMS_filename = params["LIMS_filename"] + Mutation_set_version = params["Mutation_set_version"] ) @@ -375,4 +377,4 @@ print("Writing JSON data to CSV as output-jsondata.csv") sink(NULL, type="message") # close the sink -quit() \ No newline at end of file +quit()
--- a/mykrobe_parser.xml Fri Oct 26 16:57:34 2018 -0400 +++ b/mykrobe_parser.xml Thu Apr 25 10:13:46 2019 -0400 @@ -1,4 +1,4 @@ -<tool id="mykrobe_parseR" name="mykrobe_parseR" version="0.1.3"> +<tool id="mykrobe_parseR" name="mykrobe_parseR" version="0.1.4"> <requirements> <requirement type="package" version="3.4.1">r-base</requirement> <requirement type="package" version="1.5.0">r-jsonlite</requirement>