You can use this script with the following example:
  Rscript inst/scripts/prepare_taxa.R --fil-met-pre data/interim/taxa/example_taxed.tsv.gz --org-can 1 --names-extension TRUE --names-features "row ID" --names-filename filename --names-taxon ATTRIBUTE_species

Usage:
  prepare_taxa.R [--fil-fea-raw=<fil-fea-raw>] [--fil-met-raw=<fil-met-raw>] [--fil-met-pre=<fil-met-pre>] [--gnps-id=<gnps-id>] [--names-extension=<names-extension>] [--names-features=<names-features>] [--names-filename=<names-filename>] [--names-taxon=<names-taxon>] [--org-can=<org-can>] [--org-tax=<org-tax>] [--too-met=<too-met>]

Arguments:
  fil-fea-raw                Raw features file. STRING
  fil-met-raw                OPTIONAL. If tool is "manual". Biological origin metadata file. STRING
  fil-met-pre                Taxonomically informed features file. STRING

  names-extension            The file(s) extension is present in the sample name. BOOLEAN
  names-features             Name of "feature IDs" variable in the input. STRING
  names-filename             Name of "filename" variable in the input. STRING
  names-taxon                Name of the "taxon name" variable in the input. STRING

  org-can                    Number of organisms to keep per feature. INTEGER
  org-tax                    OPTIONAL. Force all features to be attributed to given taxon. Example: "Homo sapiens". STRING

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