More than one output for EMBOSS apps

[Peter Rice]

I am looking through the output definitions for EMBOSS, with the aim of 
cleaning up some problems that especially hit interfaces that parse the 
results, and definitions of web services.

Several applications have more than one output. Some of the output files 
are optional, some are more complicated.

I would like to clean these up so that, in general, an EMBOSS 
application has only one output file (and the interface can choose the 
format)

A graph can be produced in addition to another output (seems hard to 
avoid) ... but the choices should be clearly defined so that interface 
wrappers know what they can expect.

If there is more than one output, it should be clear where this is an 
"either/or" choice - so that, for example, two wrappers can be built, 
one for each output (many interfaces do something similar with DNA and 
protein sequence input already).

More detailed thoughs in the next message.

Peter