You can use this script with the following example:
  Rscript inst/scripts/prepare_annotations_sirius.R --fil-ann-raw-sir data/interim/annotations/example_sirius/ --fil-ann-pre-can data/interim/annotations/example_canopusPrepared.tsv.gz --fil-ann-pre-for data/interim/annotations/example_formulaPrepared.tsv.gz --fil-ann-pre-str data/interim/annotations/example_siriusPrepared.tsv.gz

Usage:
  prepare_annotations_sirius.R [--fil-ann-raw-sir=<fil-ann-raw-sir>] [--fil-ann-pre-can=<fil-ann-pre-can>] [--fil-ann-pre-for=<fil-ann-pre-for>] [--fil-ann-pre-str=<fil-ann-pre-str>]

Arguments:
  fil-ann-raw-sir            Directory containing the sirius results. STRING
  fil-ann-pre-can            List of prepared canopus annotations. STRING
  fil-ann-pre-for            List of prepared formula annotations. STRING
  fil-ann-pre-str            List of prepared structural annotations. STRING
  
Options:
  -h --help                  Shows this screen.
  -v --version               Shows version.