> I'm picturing select parameter for FASTA output,
> 
> Name features using:
> * build, reference, co-ordinates and strand (default)
> * name from annotation file (if present)
> * reference name (useful if working on gene/proteins)

Agreed.

> If name is selected, then a conditional text parameter for
> GFF type files would be shown to ask which tag(s) to use
> as the name - a command separated list might work well:
> http://lists.bx.psu.edu/pipermail/galaxy-dev/2011-August/006432.html

Yes, this is a limitation of the current Galaxy framework but should be able to 
be implemented without too much trouble.

> This could default to ID for GFF3, and transcript_id,gene_id
> for GTF, and whatever else is sensible for GFF2. Or a single
> default suitable for all: ID,transcript_id,gene_id
> 
> Maybe we don't need the tag setting to be optional, just
> hard code it to something like ID,transcript_id,gene_id?

As a first step, hardcoding is fine.

> Is it acceptable for the file format conversion tools in Galaxy
> to have parameters? In this case, a list of tags to use as the
> feature name, e.g. ID, transcript_id, gene_id

Not that I know of because Galaxy assumes conversions can be done automatically 
as needed.

>> Finally, note that all changes made to any GFF code must
>> work for GFF, GFF3, and GTF formats.
> 
> That makes life interesting... what are the major sources of
> legacy GFF files within Galaxy (anything not GFF3)?

Perhaps I spoke a bit too strongly here. I think that GTFs are the primary 
flavor of GFF files used in Galaxy, and these are acquired from UCSC and 
Ensembl. GFF3 also seem to be used quite frequently as well, especially for 
folks working with bacteria and other simple organisms. GFF 2.2 and earlier 
aren't seen much as best I know.

So let me rephrase and say that any changes need to be compatible with GTF and 
GFF3.

Best,
J.
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