Y and N args

[Edgar Crowdy]

Hi,

I have a question about the standards for yes/no options in EMBOSS
programs.  

dotpath works as I expect it to.  There are three Y/N parameters: "data",
"overlap" and "boxit".  On the command line I represent them like this:
-nodata -overlaps -boxit  (meaning 'no' to the first and 'yes' to the last
two).  In other words, the command line switch on its own is a 'yes', and
to say 'no' you prepend 'no' to the switch.

I'm having trouble with a program called cirdna.  In that program I can
use "-noticklines" and "-nointersymbol" but I can't express a 'yes' by
saying -ticklines or -intersymbol as in other programs.  It only runs if I
say '-intersymbol Y', for example.

Is cirdna an exception to the rule or are there other programs?
Will placing a Y or N after all Y/N parameters work?

I need a standard that works for all EMBOSS programs with Y/N parameters.

-- 
Edgar Crowdy, Programmer                crowdy at bioinfo.sickkids.on.ca 
Centre for Computational Biology, Hospital for Sick Children, Toronto