--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cameradims.R	Thu May 10 07:20:04 2018 -0400
@@ -0,0 +1,123 @@
+library(optparse)
+library(cameraDIMS)
+
+option_list <- list(
+  make_option(c("-i", "--in_file"), type="character"),
+  make_option(c("-o", "--out_dir"), type="character"),
+  make_option("--ppm_iso", default=5),
+  make_option("--ppm_adduct", default=5),
+  make_option("--maxiso", default=4),
+  make_option("--mzabs_iso", default=0.015),
+  make_option("--mzabs_adduct", default=0.015),
+  make_option("--maxcharge", default=3),
+  make_option("--maxmol", default=3),
+  make_option("--polarity", default='pos'),
+  make_option("--rule_path"),
+  make_option("--rule_type"),
+  make_option("--export_ruleset", action="store_true"),
+  make_option("--intensity_filter", default=0)
+)
+
+
+# store options
+opt<- parse_args(OptionParser(option_list=option_list))
+
+print(sessionInfo())
+print(opt)
+
+df <- read.table(opt$in_file, header = TRUE, sep='\t', stringsAsFactors=FALSE)
+
+print('IN DATA')
+print(nrow(df))
+print(head(df))
+
+devppm_adduct <- opt$ppm_adduct / 1000000
+devppm_iso <- opt$ppm_iso / 1000000
+
+paramiso <- list("ppm"=opt$ppm_iso,
+                 "filter"=TRUE,
+                 "maxcharge"=opt$maxcharge,
+                 "maxiso"=opt$maxiso,
+                 "mzabs"=opt$mzabs_iso,
+                 "intval"='maxo',
+                 "minfrac"=0.5,
+                 'IM'=NULL,
+                 'devppm'=devppm_iso)
+
+paramadduct <- list("maxCharge"= opt$maxcharge,
+                    "maxMol"= opt$maxmol,
+                    'devppm'=devppm_adduct,
+                    "mzabs"=opt$mzabs_adduct,
+                    'IM'=NULL,
+                    "filter"=TRUE,
+                    'ppm'=opt$ppm_adduct,
+                    "quasimolion"= c(1, 6, 8),
+                    'polarity'=opt$polarity)
+
+
+
+
+if(is.null(opt$export_ruleset)){
+    rule_export <- FALSE
+}else{
+    rule_export <- TRUE
+}
+
+df$mz <- as.numeric(df$mz)
+
+print(head(df$mz))
+
+if ('intensity' %in% colnames(df)){
+    colnames(df)[colnames(df)=='intensity'] = 'i'
+}
+
+if (!'peakID' %in% colnames(df)){
+    df <- cbind('peakID'=1:nrow(df), df)
+}
+
+df$i <- as.numeric(df$i)
+
+df <- df[df$i>opt$intensity_filter,]
+
+if (nrow(df)==0){
+   print('No peaks left after filtering')
+   quit()
+}
+
+
+if (opt$rule_type=='extended_large'){
+
+   rule_sep=','
+   opt$rule_type <- 'user'
+   if(opt$polarity=='pos'){
+	opt$rule_path <-  system.file("rules", "CAMERA_rules_PosFinal_PlusLi.csv", package = "cameraDIMS")
+   }else{
+	opt$rule_path <-  system.file("rules", "CAMERA_rules_NegFinal_PlusLi.csv", package = "cameraDIMS")
+   }   
+}else{
+   rule_sep='\t'
+}
+
+cameraOut <- cameraDIMS(data=df,
+                        params_iso=paramiso,
+                        params_adduct=paramadduct,
+                        rule_type=opt$rule_type,
+                        rule_pth=opt$rule_path,
+                        rule_sep=rule_sep,
+                        rule_export=rule_export)
+
+
+print(head(cameraOut[[1]]))
+print(head(cameraOut[[2]]))
+
+
+out_file1 <- file.path(opt$out_dir, 'camera_annotated_peaklist.txt')
+out_file2 <- file.path(opt$out_dir, 'camera_annotated_map.txt')
+out_file3 <- file.path(opt$out_dir, 'ruleset.txt')
+
+write.table(cameraOut[[1]], out_file1, row.names=FALSE, sep='\t')
+write.table(cameraOut[[2]], out_file2, row.names=FALSE, sep='\t')
+
+if (rule_export){
+    write.table(cameraOut[[3]], out_file3, row.names=FALSE, sep='\t')
+}