You can use this script with the following example:
  Rscript inst/scripts/prepare_annotations_gnps.R --fil-ann-raw-spe-gnp data/interim/annotations/example_gnps.tsv --fil-ann-pre-str data/interim/annotations/example_gnpsPrepared.tsv.gz

Usage:
  prepare_annotations_gnps.R [--=fil-ann-pre-str<fil-ann-pre-str>] [--gnps-id=<gnps-id>] [--gnps-workflow=<gnps-workflow>]

Arguments:
  fil-ann-raw-spe-gnp        List of GNPS spectral matching results. STRING
  fil-ann-pre-str            List of prepared structural annotations. STRING

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