gistfile1.txt

library(optparse)

##################### Options ########################
opts=list(
  make_option("--project", action="store", default="", type="character", help="Project (default: none)"),
  make_option("--mc", action="store", default=3, type="integer", help="Min cells (default: 3)"),  
  make_option("--resolution", action="store", default=0.8, type="numeric", help="Resolution value (default: 0.8)"),
  make_option("--usehvg", action="store", default=TRUE, type="logical", help="Use HVG? (default: TRUE")
)
opts=parse_args(OptionParser(option_list=opts))

if (opts$indropsdata == "") {
  cat("\n")
  message("Error: --indropsdata parameter must be provided. See script usage (--help)")
  quit()
}

message("Options: \n")
print(opts)