diff track_rt_raw.R @ 12:cb8dce9812ff draft

planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f79fa34772bbab836d89cf8bad52d49285409a98

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/track_rt_raw.R	Thu Jun 14 09:19:47 2018 -0400
@@ -0,0 +1,28 @@
+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')
+}