Mercurial > repos > computational-metabolomics > mspurity_flagremove

diff filterFragSpectra.R @ 7:69ed543767b2 draft

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"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit e3b17490a958d80ebe78ef1bebebef48948e1240"
author computational-metabolomics
date Tue, 08 Feb 2022 13:52:56 +0000
parents a67b129cd78e
children a0ee43397d1e
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--- a/filterFragSpectra.R	Thu Mar 04 12:30:15 2021 +0000
+++ b/filterFragSpectra.R	Tue Feb 08 13:52:56 2022 +0000
@@ -17,7 +17,8 @@
   make_option("--snr", default = 0.0),
 
   make_option("--rmp", action = "store_true"),
-  make_option("--snmeth", default = "median", type = "character")
+  make_option("--snmeth", default = "median", type = "character"),
+  make_option("--allfrag", action = "store_true")
 )
 
 opt <- parse_args(OptionParser(option_list = option_list))
@@ -39,12 +40,19 @@
   opt$rmp <- TRUE
 }
 
+if (is.null(opt$allfrag)) {
+  opt$allfrag <- FALSE
+}else{
+  opt$allfrag <- TRUE
+}
+
 pa <- filterFragSpectra(pa,
                         ilim = opt$ilim,
                         plim = opt$plim,
                         ra = opt$ra,
                         snr = opt$snr,
                         rmp = opt$rmp,
+                        allfrag = opt$allfrag,
                         snmeth = opt$snmeth)
 
 print(pa)