--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/plasmidprofile.R	Fri Feb 03 16:34:16 2017 -0500
@@ -0,0 +1,59 @@
+#' RScript capable
+#' Rscript plasmidprofile.R -b blast_runG.tsv -s srst2_runG.tsv -u 0.75 -l 10000 -t "This is a test" -a
+
+
+suppressPackageStartupMessages(library("optparse"))
+suppressPackageStartupMessages(library("Plasmidprofiler"))
+options(bitmapType='cairo')
+
+cl_arguments <- function(){
+  # CL arguments ####
+  option_list = list(
+    make_option(c("-b", "--blastfile"), type="character", default=NULL,
+                help="BLAST TSV file name", metavar="character"),
+    make_option(c("-s", "--srst2file"), type="character", default=NULL,
+                help="SRST2 TSV file name", metavar="character"),
+    make_option(c("-u", "--sureness"), type="numeric", default=NA,
+                help="Sureness cut off [default = %default]", metavar="numeric"),
+    make_option(c("-c", "--coverage"), type="numeric", default=NA,
+                help="Percent coverage cut off", metavar="numeric"),
+    make_option(c("-l", "--length"), type="numeric", default=NA,
+                help="Plasmid length cut off", metavar="numeric"),
+    make_option(c("-a", "--anonymize"), action="store_true", default=NA,
+                help="Anonymize plasmid and sample names"),
+    make_option(c("-o", "--outfile"), type="character", default="P2Run_",
+                help="Output filename prefix [default=  %default]", metavar="character"),
+    make_option(c("-t", "--title"), type="character", default="Plasmid Profiles",
+                help="Title of image [default = %default]", metavar="character"),
+    make_option(c("-C", "--combineincs"), action="store_true", default=NA,
+                help="Combine very closely related incompatibility groups. eg. ")
+    # make_option(c("-T", "--Test"), action="store_true", default=NA,
+    #             help="Test filecache")
+
+  );
+
+  opt_parser <- OptionParser(option_list=option_list);
+  opt <- parse_args(opt_parser);
+
+  if (is.null(opt$blastfile) | is.null(opt$srst2file)){
+    print_help(opt_parser)
+    stop("SRST2 and BLAST files must be supplied.", call.=FALSE)
+  }
+  opt
+}
+
+
+opt <- cl_arguments()
+
+filecache <<- new.env(parent = .GlobalEnv)
+assign("name", opt$outfile, envir = filecache)
+assign("mods", "Subsampling applied: ", envir = filecache)
+
+main(blast.file = opt$blastfile,
+     srst2.file = opt$srst2file,
+     coverage.filter = opt$coverage,
+     sureness.filter = opt$sureness,
+     length.filter = opt$length,
+     anonymize = opt$anonymize,
+     combine.inc = opt$combineincs,
+     main.title = opt$title)