So I'm continuing to run into issues with BED vs BED12 files due to
Galaxy automatically converting GFF/GTF files to non-BED12 files.
Essentially, the RSeQC tools require BED12 files, but Galaxy allows
users to use GTF/GFF files which it automatically converts incorrectly.
Is there any desire/
Well, I somewhat follow you. My main goal would be to allow people to
use GTF files in the RSeQC tools. My initial thought was to write a tool
to convert GTF to BED12 (which I've done). However, it would be really
nice to have Galaxy be able to automatically convert behind the scenes.
The probl
Hi Lance,
Ah, yes, using bed12 would be problematic, as all bedstrict types are currently
set to not be uploadable or datatype assignable. This stems from a long history
of abuse of the BED format in Galaxy (where datasets should have been generic
‘interval’ matching bed metadata of chrome,star
Thanks for the info Dan. I've explored using bed12, but I have a few
questions.
1. When attempting to use 'bed12' or 'Bed12' as a file type in a test, I
get the following error:
Exception: {u'message': {u'type': u'error', u'data': {u'file_type':
u"An invalid option was selected for file_
Hi Lance,
FWIW, there is an existing bedstrict and bed12 (and bed6) datatypes in Galaxy.
The strict datatypes are currently usually created by implicit datatype
converters and are most often used by some external display applications that
need standards conforming files. bed6/12 are subclasses
Does anyone know of any efforts to create a BED12 datatype for Galaxy?
Since some tools require BED12 and the automatic convertion from
GFF-to-BED does not seem to generate a BED12, it seems it might be a
worthwhile addition.
If not, what would be the best way to go about doing this? Making it
