On Thu, Jul 17, 2014 at 5:45 PM, Björn Grüning
<bjoern.gruen...@gmail.com> wrote:
> Hi,
> I think you are right John. Datatypes have many issues in that regard as I
> can tell, from a few bug reports. Imho datatypes should be handled like
> "Tool dependency definitions". There should be only one "installable
> revsion".
> But that aside, emboss datatypes are already broken. For example asn1 was
> added into Galaxy but it still exists in emboss_datatypes.
> Moreover, howto add a proper genbank datatype with sniffer, split and merge
> functions? Ideally, every datatype should have its own repository, but that
> is an overhead I would like to omit ... any other ideas?
> I would love to discuss that issue further, maybe a hangout with Greg and
> Peter?
> Thanks John for your input,
> Bjoern

This could be high level, e.g. "other sequence file formats" repository
covering GenBank, EMBL, SwissProt plain text, UniProt XML, etc;
one for multiple sequence alignments; one for EMBOSS' own output...

But it wouldn't be that much more work to do one ToolShed repo
per additional file format, would it?

One reason I have been meaning to do some of these is familiarity with
many of these formats from looking after/writing parsers in Biopython.

Having this done sooner rather than later ought to head off too many
incompatible datatype names which worries me. Is it too late to adopt
something like the EDAM ontology for the datatypes within Galaxy?


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