More than one output for EMBOSS apps

Peter Rice pmr at
Mon Mar 24 15:20:43 UTC 2003

Martin Senger wrote:
>>I (and the others as well) consider the ACD files useful also
> for the non-emboss applications which one cannot clean up and which still
> may produce several outputs. The ACD file syntax, therefore, in my
> opinion, should keep the possibility to specify more outputs - even though
> this will not be used by the emboss appls themselves.

Yes indeed.

I am planning something with the working title "ACIDIFY" which will be 
an ACD syntax wrapper around other applications.

ACIDIFY will validate the inputs (for example, blast database name, 
blast gap penalty options), and convert input and output formats.

Imagine blast as an EMBOSS application (or more likely as several EMBOSS 
applications). A wrapper (for example SoapLab) could define inputs and 
outputs in the same way as for any other EMBOSS application.

The validation may be complicated ... but only if we allow the full 
horrors of a blast gap penalty options, rather than a list of valid 
combinations :-)

Additional data types should map on to existing ACD types. For example, 
blast databases could be presented as a list of valid strings. ACIDIFY 
will check what blast databases a service provider has. It could easily 
report that list to as service user so they know what options to make 
available. It could also report the release number, number of entries, 
or other properties.

The complicated part if the validation, of course.

A list of useful non-EMBOSS applications to "acidify" would be a great help.



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