Mercurial > repos > tomnl > create_sqlite_db
comparison track_rt_raw.R @ 4:ff61a6fb23bf draft
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 9ea2ca0892fa55c21491c93afba790e8d9427e01-dirty
| author | tomnl |
|---|---|
| date | Wed, 04 Apr 2018 17:08:30 -0400 |
| parents | 1a88758357ed |
| children |
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| 3:2766f2a85997 | 4:ff61a6fb23bf |
|---|---|
| 1 library(optparse) | 1 library(optparse) |
| 2 library(xcms) | 2 |
| 3 print(sessionInfo()) | 3 print(sessionInfo()) |
| 4 | 4 |
| 5 option_list <- list( | 5 option_list <- list( |
| 6 make_option(c("--xset_path"), type="character"), | 6 make_option(c("--xset_path"), type="character"), |
| 7 make_option(c("-o", "--out_dir"), type="character") | 7 make_option(c("-o", "--out_dir"), type="character"), |
| 8 make_option(c("--extract_peaks"), action="store_true") | |
| 8 ) | 9 ) |
| 9 | 10 |
| 10 # store options | 11 # store options |
| 11 opt<- parse_args(OptionParser(option_list=option_list)) | 12 opt<- parse_args(OptionParser(option_list=option_list)) |
| 12 | 13 |
| 19 xset@peaks <- cbind(xset@peaks, rtraw) | 20 xset@peaks <- cbind(xset@peaks, rtraw) |
| 20 | 21 |
| 21 | 22 |
| 22 print('saving RData') | 23 print('saving RData') |
| 23 save.image(file.path(opt$out_dir, 'xset_rt_raw_tracked.RData')) | 24 save.image(file.path(opt$out_dir, 'xset_rt_raw_tracked.RData')) |
| 25 | |
| 26 if(!is.null(opt$extract_peaks)){ | |
| 27 write.table(xset@peaks, file.path(opt$out_dir, 'xset_peaks.tsv'), row.names=FALSE, sep='\t') | |
| 28 } |