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view track_rt_raw.R @ 4:7e633c70fdfc draft

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planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
author tomnl
date Fri, 30 Mar 2018 10:10:38 -0400
parents 146699c00d38
children faba6cd56875
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library(optparse)
library(xcms)
print(sessionInfo())

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

# 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'))