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#' 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"))
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)
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