You can use this script with the following example:
  Rscript inst/scripts/filter_annotations.R

Usage:
  filter_annotations.R [--fil-ann-fil=<fil-ann-fil>] [--fil-ann-pre-str=<fil-ann-pre-str>] [--fil-fea-pre=<fil-fea-prer>] [--fil-lib-tem-pre=<fil-lib-tem-pre>] [--ms-tol-rt-lib=<ms-tol-rt-lib>]

Arguments:
  fil-ann-fil                Filtered annotation file. STRING
  fil-ann-pre-str            List of prepared structural annotations. STRING
  fil-fea-pre                Prepared features file. STRING
  fil-lib-tem-pre            List of prepared temporal libraries. STRING

  ms-tol-rt-lib              Retention time tolerance for library in minutes. FLOAT

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