You can use this script with the following example:
Rscript inst/scripts/prepare_libraries_rt.R --fil-lib-tem-exp-csv data/source/libraries/rt/internal.tsv --fil-lib-tem-is-csv data/source/libraries/rt/predicted.tsv --fil-lib-tem-pre data/interim/libraries/rt/prepared.tsv.gz

Usage:
  prepare_libraries_rt.R [--fil-lib-tem-exp-csv=<fil-lib-tem-exp-csv>] [--fil-lib-tem-exp-mgf-neg=<fil-lib-tem-exp-mgf-neg>] [--fil-lib-tem-exp-mgf-pos=<fil-lib-tem-exp-mgf-pos>] [--fil-lib-tem-is-csv=<fil-lib-tem-is-csv>] [--fil-lib-tem-is-mgf-neg=<fil-lib-tem-is-mgf-neg>] [--fil-lib-tem-is-mgf-pos=<fil-lib-tem-is-mgf-pos>] [--fil-lib-tem-pre=<fil-lib-tem-pre>] [--names-inchikey=<names-inchikey>] [--names-mgf-ik=<names-mgf-ik>] [--names-mgf-rt=<names-mgf-rt>] [--names-mgf-sm=<names-mgf-sm>] [--names-rt-lib=<names-rt-lib>] [--names-smiles=<names-smiles>] [--units-rt=<units-rt>]

Arguments:
  fil-lib-tem-exp-csv        List of experimental temporal libraries (CSV). STRING
  fil-lib-tem-exp-mgf-neg    List of negative experimental temporal libraries (MGF). STRING
  fil-lib-tem-exp-mgf-pos    List of positive experimental temporal libraries (MGF). STRING
  fil-lib-tem-is-csv         List of in silico temporal libraries (CSV). STRING
  fil-lib-tem-is-mgf-neg     List of negative in silico temporal libraries. (MGF) STRING
  fil-lib-tem-is-mgf-pos     List of positive in silico temporal libraries (MGF). STRING
  fil-lib-tem-pre            List of prepared temporal libraries. STRING

  names-inchikey             Name of "InChIKey" variable in the input. STRING
  names-mgf-ik               Name of "InChIKey" in MGF. STRING
  names-mgf-rt               Name of "retention time" in MGF. STRING
  names-mgf-sm               Name of "SMILES" in MGF. STRING
  names-rt-lib               Name of "retention time" variable (lib) in the input. STRING
  names-smiles               Name of "SMILES" variable in the input. STRING

  units-rt                   Unit of the "retention time" variable in the input. Must be "seconds" or "minutes". STRING

Options:
  -h --help                  Shows this screen.
  -v --version               Shows version.