Hi,
The following tiny patch adds a light-gray visual cue in the html form, to give a better idea as to which parameters go together.
It looks acceptable even with nested <conditional> parameters.
See it in action here: http://cancan.cshl.edu/publicgalaxy/root?tool_id=cshl_bowtie_pe1 http://cancan.cshl.edu/publicgalaxy/root?tool_id=cshl_tophat_pe1
It might not be the prettiest thing, but it works nicely with minimal code changes.
Patch is here: http://cancan.cshl.edu/labmembers/gordon/files/conditional-group-css2.patch
Comments are welcomed, -gordon