Mercurial > repos > tomnl > create_sqlite_db

diff track_rt_raw.R @ 4:ff61a6fb23bf 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 17:08:30 -0400
parents 1a88758357ed
children
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--- a/track_rt_raw.R	Fri Mar 30 10:12:19 2018 -0400
+++ b/track_rt_raw.R	Wed Apr 04 17:08:30 2018 -0400
@@ -1,10 +1,11 @@
 library(optparse)
-library(xcms)
+
 print(sessionInfo())
 
 option_list <- list(
   make_option(c("--xset_path"), type="character"),
-  make_option(c("-o", "--out_dir"), type="character")
+  make_option(c("-o", "--out_dir"), type="character"),
+  make_option(c("--extract_peaks"), action="store_true")
 )
 
 # store options
@@ -21,3 +22,7 @@
 
 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')
+}