For inexperienced users, it might be difficult to see which options for a smrt command is required
and which ones are optional.
With a growing number of options, the smrt subcommand -h can become somewhat overwhelming, especially for first time users. Especially options like custom names for output files might not be very interesting for many users.
Possibilities to tackle this could be:
Group the output of smrt subcommand -h into two categories: required and optional. We would have to think about how to display either-or options (e,g, taxize can take either a names list or a root taxon).
alternatively, we could add (optional) or (required) before or after the description of each option.
Options and arguments could be color-coded when invoking smrt subcommand -h
For inexperienced users, it might be difficult to see which options for a
smrtcommand is required and which ones are optional. With a growing number of options, thesmrt subcommand -hcan become somewhat overwhelming, especially for first time users. Especially options like custom names for output files might not be very interesting for many users.Possibilities to tackle this could be:
smrt subcommand -hinto two categories: required and optional. We would have to think about how to display either-or options (e,g, taxize can take either a names list or a root taxon).(optional)or(required)before or after the description of each option.smrt subcommand -h...