ACD not always required parameters

[Peter Rice]

gbottu at ben.vub.ac.be wrote:
> Remains the problem of the required parameters. I send an 
> example as attachment.

The data type is seqall. This will need a value. No value (empty default) 
means it tries to read nothing.

It is a seqall (or sequence or seqset) that needs a value, the 'required' 
part is not important ... except of course if it is 'required' the user 
will be prompted.

> You will note that the fields "userdb" and "userfastadb" have no reasonable 
> default. The one I had to add is an awfull hack. But delete default and run 
> "acdc fasta", you will get an error.

The big problem here is trying to fit all the FASTA programs into one ACD file,
instead of using 9 files.

I did consider some time back extending ACD syntax to cover launching 
external applications with an ACD interface. There is an outline syntax 
definition including additional validation for (for example) blast gap 
penalties. The tricky part is testing the input is valid where it is a 
strange database (blast for example) before launching the application.

Can anyone help with defining requirements for blast/fasta/etc.

regards,

Peter

-- 
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Peter Rice, LION Bioscience Ltd, Cambridge, UK
peter.rice at uk.lionbioscience.com +44 1223 224723