Mercurial > repos > tomnl > assess_purity_msms

view track_rt_raw.R @ 23:c5ba85825284 draft

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planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 04023134d8f28e85927ca293373c506484149ead-dirty
author tomnl
date Fri, 01 Jun 2018 15:28:32 -0400
parents faba6cd56875
children
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library(optparse)

print(sessionInfo())

option_list <- list(
  make_option(c("--xset_path"), type="character"),
  make_option(c("-o", "--out_dir"), type="character"),
  make_option(c("--extract_peaks"), action="store_true")
)

# store options
opt<- parse_args(OptionParser(option_list=option_list))

load(opt$xset_path)

print(xset)

rtraw <- xset@peaks[,c('rt', 'rtmin', 'rtmax')]
colnames(rtraw) <- c('rt_raw','rtmin_raw','rtmax_raw')
xset@peaks <- cbind(xset@peaks, rtraw)


print('saving RData')
save.image(file.path(opt$out_dir, 'xset_rt_raw_tracked.RData'))

if(!is.null(opt$extract_peaks)){
    write.table(xset@peaks, file.path(opt$out_dir, 'xset_peaks.tsv'), row.names=FALSE, sep='\t')
}