R {optparse} using trailing arguments

optparse_with_trailing_args.R

# My rscript template assumes all command line arguments are in option-form
# `Rscript <script_name> --logical_option --some_flag some_value --some_other_flag some_other_value`
#
# When you want to pass a variable number of files into your script, the option-form doesn't work well
# so it's better to use trailing arguments
# `Rscript <script_name> --some_option --flag with_value trailing1 trailing2 trailing3 ...`
#
# optparse works well in the latter case:

library(magrittr)
library(optparse)

define_parser <- function() {
  description <- "Describe my script"
  parser <- OptionParser(
    usage = "%prog [options] files", description = description
  ) %>%
    add_option("--some_option", action = "store_true", default = FALSE) %>%
    add_option("--flag", type = "double")
  
  parser
}

####

main <- function(opt) {
  options <- opt[["options"]]
  files <- opt[["args"]]
  
  run_script(
    input_files = files,
    use_option = options[["some_option"]],
    flag_value = options[["flag"]]
  )
}

####

test <- function() {
  # define tests
}

####

opt <- optparse::parse_args(define_parser(), positional_arguments = TRUE)

if (opt[["options"]][["test"]]) {
  test()
} else {
  main(opt)
}