Adjust parameter metadata for Jabaws alignment services

A couple of parameters to Jabaws services appear to be misconfigured:

'Another order of sequence in output alignment' (MSAProbs, GLProbs)
- is marked as required, with options --alignment and -a and no default
- these seem to be aliases, not alternatives (http://msaprobs.sourceforge.net/homepage.htm#parameters)
- should instead be an optional flag '--alignment' (like Probcons 'Output aligned')

'CLUSTAL format for output alignment' (MSAProbs, GLProbs)
- is marked as required, with option -clustalw, no default
- should instead be optional

Correcting these would remove a blocker for JAL-2985: don't show a checkbox for required options (shouldn't be possible to deselect them).
The Jalview dialog could then show the above as simple checkboxes instead of dropdown choices.