Matt has already started working on this, but I wanted to summarize the effort in an issue:
Digestion tab:
--pep-digest-enzyme="<enzyme-name>"
--pep-max-missed-cleavages=<num> (1-... defaults to 0)
--background-proteome-name=<name>
--background-proteome-file=<path/to/file.protdb>
--pep-unique-by=<None | Proteins | Genes | Species>

Filter tab:
--pep-min-length=<num>
--pep-max-length=<num>
--pep-exclude-nterminal-aas=<num>
--pep-exclude-potential-ragged-ends