remarks about ACD syntax

Guy Bottu gbottu at
Mon Aug 26 15:52:32 UTC 2002

from : BEN

	Dear colleagues,
I have started to port under EMBOSS some local developements we had under GCG at 
the BEN site. I wrote some ACD files (under EMBOSS 2.4.1) and I bumped on some 
limitations of the syntax.
- the return value of a "list" or "select" cannot be used in computations for 
other fields. Yet, this would be veru useful. E.g. for integrating BLAST under 
EMBOSS you could first have a select with blastn/blastp/blastx/tblastn/tblastx 
that would control the default values of all the other parameters.
- some parameters can be "required" or not, depending on other parameters. When 
a parameter is sometimes required however, it is necessary to provide a default 
value, otherwise an error message will appear when you run the program via 
selections that do not involve that parameter. The ACD documentation mentions a 
"missing" attribute, but this seems not to work.
- a parameter of the type "outfile" leads always to the creation of a file, even 
when the outfile is optional. An example : when you run dan -plot, an empty file
xxx.dan is created.

Am I wrong ? And if not, can we expect a future version with more flexible 
syntax ?

	Guy Bottu

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