cli-args.R

library(optparse)

# ------------------------------------------------------------------------------
# defaults
# ------------------------------------------------------------------------------

default.nthreads <- 1
default.verbose <- FALSE

# ------------------------------------------------------------------------------
# parsing arguments
# ------------------------------------------------------------------------------

options <- list (

  make_option(
    opt_str = c("-t", "--threads"),
    dest    = "nthreads",
    type    = "integer",
    default = default.nthreads,
    help    = paste0("number of threads to use, defaults to ", default.nthreads),
    metavar = "4"),

  make_option(
    opt_str = c("-v", "--verbose"),
    action  = "store_true",
    default = default.verbose,
    help    = "print more output on what's happening")

)

parser <- OptionParser(
  usage       = "Rscript %prog [options] input output",
  option_list = options,
  description = "\nan awesome R script",
  epilogue    = "use with caution, the awesomeness might slap you in the face!"
)

cli <- parse_args(parser, positional_arguments = 2)

# ------------------------------------------------------------------------------
# assign a few shortcuts
# ------------------------------------------------------------------------------

verbose <- cli$options$verbose
input   <- cli$args[1]
output  <- cli$args[2]

# ------------------------------------------------------------------------------
# actual program
# ------------------------------------------------------------------------------

if (verbose) {
  cat("[info] listing options now ...\n")
}

cat(paste0("number of threads: ", cli$options$nthreads, "\n"))
cat(paste0("input: ", input, "\n"))
cat(paste0("output: ", output, "\n"))

if (verbose) {
  cat("[info] end of script\n")
}