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comparison track_rt_raw.R @ 4:a8d243fcf676 draft

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planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 9ea2ca0892fa55c21491c93afba790e8d9427e01-dirty
author tomnl
date Wed, 04 Apr 2018 16:34:45 -0400
parents 26fd52ed6d21
children
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3:31c68f2d97b5 4:a8d243fcf676
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 }