Thanks, the gtf sniffer was not in the datatypes_conf.xml.sample so I assumed it did not exist. I have updated this to include the gtf sniffer but my file is still not being recognised. I have attached the file, any help would be great. Thanks Shaun Quoting Jeremy Goecks <jeremy.goecks@emory.edu>:
I know gff and gtf are very similar but is it possible to have a gtf sniffer?
There is a GTF sniffer in Galaxy, and it should detect GTF files as such assuming your datatypes_conf.xml file is set up appropriately. To correctly sniff GTF files, make sure you have the following line in your <sniffers> section and that it appears above the GFF entry:
... <sniffer type="galaxy.datatypes.interval:Gtf"/> <sniffer type="galaxy.datatypes.interval:Gff"/> <sniffer type="galaxy.datatypes.interval:Gff3"/> ...
If you have a GTF file that's still not being recognized, please send it our way and we'll take a look.
Out of interest is there any documentation relating to writing sniffers for different datatypes I should probably have a go at writing a few for my on.
I don't see anything in our wiki off hand. However, if you're going to write your own, looking at an existing sniffer should make it clear what needs to happen. For instance, see any of the sniff() functions in /lib/galaxy/datatypes/interval.py
Best, J.
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