This problem seems to be specific to OSX.

The three parameters, "Preserve reading frame", "Reading frames" and "Append number" don't work when set in the
bioLegato menu.

First, we need to determine that the do work when running
the binary at the command line. If they do, then we assume
it is a problem with the ribosome.item file. It is most likely
an issue with how OSX parses shell commands. The
itemmethod is a particualarly complex one.

Therfore, the most likely solution is to move most of the
shell code out of the itemmethod and into a shell script.