Mercurial > repos > tomnl > msp_split

diff track_rt_raw.R @ 5:f2683ec717fe draft default tip
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit a164f06c09dc1614c2909c247ebf390aab433527-dirty
author: tomnl
date: Wed, 18 Sep 2019 05:46:09 -0400
parents: 769ec2496d14
--- a/track_rt_raw.R	Wed Jul 18 06:04:14 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,28 +0,0 @@
-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')
-}