Make more distinction between source and sink options when parsing CLI input

[caufieldjh]

Describe the bug
get_source and get_sink in transformer.py (and possibly elsewhere) check the same value for format in the CLI.
This makes the assumption that all sources are also valid sinks and vice versa, which may not always be true, and may cause commands to fail if a name of a sink is not in the source map.
One solution - combine the source and sink map into something tracking source/sink status of all options.
Or, check both maps when parsing CLI input.