You can use this script with the following example:
  Rscript inst/scripts/prepare_libraries_sop_lotus.R --fil-lib-sop-raw-ecm data/source/libraries/sop/lotus.csv.gz --fil-lib-sop-pre data/interim/libraries/sop/lotus_prepared.tsv.gz

Usage:
  prepare_libraries_sop_ecmdb.R [--fil-lib-sop-raw-ecm=<fil-lib-sop-raw-ecm>] [--fil-lib-sop-pre=<fil-lib-sop-pre>]

Arguments:
  fil-lib-sop-raw-lot        LOTUS raw structure organism pairs library. STRING
  fil-lib-sop-pre            List of prepared structure organism pairs libraries. STRING

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