You can use this script with the following example:
  Rscript inst/scripts/create_edges_spectra.R --fil-spe-raw data/source/examples/spectra.mgf --fil-net-spe-edg-raw data/interim/features/example_edgesSpectra.tsv.gz --ms-tol-mas-dal-ms2 0.01 --ms-tol-mas-ppm-ms2 10 --ann-thr-ms2-sim-edg 0.7 --ms-thr-ms2-int 5

Usage:
  create_edges_spectra.R [--ann-thr-ms2-sim-edg=<ann-thr-ms2-sim-edg>] [--fil-net-spe-edg-raw=<fil-net-spe-edg-raw>] [--fil-spe-raw=<fil-spe-raw>] [--ms-thr-ms2-int=<ms-thr-ms2-int>] [--ms-tol-mas-ppm-ms2=<ms-tol-mas-ppm-ms2>] [--ms-tol-mas-dal-ms2=<ms-tol-mas-dal-ms2>] [--ms-tol-rt-min=<ms-tol-rt-min>]

Arguments:
  ann-thr-ms2-sim-edg        Similarity threhsold for edges. FLOAT

  fil-net-spe-edg-raw        Raw edges file. STRING
  fil-spe-raw                Raw spectral file. STRING

  ms-thr-ms2-int             Intensity threshold for MS2. INTEGER
  ms-tol-mas-ppm-ms2         Relative mass tolerance for MS2 in ppm. FLOAT
  ms-tol-mas-dal-ms2         Absolute mass tolerance for MS2 in Dalton. FLOAT
  ms-tol-rt-min              Retention time tolerance in minutes. FLOAT

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