--- a/createMSP.R	Wed Apr 01 11:19:15 2020 -0400
+++ b/createMSP.R	Thu Apr 09 14:28:45 2020 -0400
@@ -15,6 +15,7 @@
   make_option("--intensity_ra",type="character"),
   make_option("--include_adducts",type="character"),
   make_option("--msp_schema",type="character"),
+  make_option("--include_adducts_custom",type="character", default=""),
   make_option("--out_dir",type="character", default=".")
 )
 opt <- parse_args(OptionParser(option_list=option_list))
@@ -66,17 +67,33 @@
   xcms_groupids <- trimws(strsplit(opt$xcms_groupids, ',')[[1]])
 }
 
+
+
+
+
+if (is.null(opt$include_adducts_custom)){
+  include_adducts_custom <- ''
+}else{
+  include_adducts_custom <- opt$include_adducts_custom
+}
+
+
 if (opt$include_adducts=='None'){
   include_adducts <- ''
 }else{
   include_adducts <- opt$include_adducts
-  include_adducts <- gsub("__ob__", "[", include_adducts)
-  include_adducts <- gsub("__cb__", "]", include_adducts)
-  include_adducts <- trimws(include_adducts)
+}
+
+include_adducts_all <- paste(include_adducts_custom, ',', include_adducts, sep="")
 
-  include_adducts <- gsub(",", " ", include_adducts)
+include_adducts_all <- gsub("^,", "", include_adducts_all)
+include_adducts_all <- gsub(",$", "", include_adducts_all)
 
-}
+include_adducts_all <- gsub("__ob__", "[", include_adducts_all)
+include_adducts_all <- gsub("__cb__", "]", include_adducts_all)
+include_adducts_all <- trimws(include_adducts_all)
+include_adducts_all <- gsub(",", " ", include_adducts_all)
+
 
 
 if(is.null(opt$filter)){
@@ -96,7 +113,7 @@
                     xcms_groupids = xcms_groupids,
                     filter = filter,
                     intensity_ra=opt$intensity_ra,
-                    include_adducts=include_adducts,
+                    include_adducts=include_adducts_all,
                     msp_schema=opt$msp_schema)
 
 print('msp created')