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 problem there is that it already does conversion from GTF to BED,
but not to BED12. Another option would be to include the conversion as
part of the tools, but that is kinda messy and doesn't help any other
tools that need the same thing.
I'm open to suggestions on how to handle this, but right now, the only
option I can see is to build the conversion in as part of the tool,
correct? I'm not quite sure why allowing users to specify BED12 vs BED6
vs "BED" is any worse than the way things work with other datatypes
(fastq, fastqsanger, etc.), but I realize you guys have a lot of
experience with users that I don't.
Lance
Daniel Blankenberg wrote:
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,start,end of 1,2,3). I added these datatypes to force
conversions of bed/interval files to Real bed/6/12 files, especially
as needed by external visualization tools --- that way you can click
on a 'bed' (fake) file and Galaxy will convert it to Real bed and load
the external service, or run the Galaxy tool on the properly formatted
data.
Basically, there are restrictions in place to try to ensure that a
bedstrict datatype is actually BED conforming. I am open to loosening
these restrictions up, however, and allowing them to function as
'normal' datatypes (users would be free to shoot themselves in the
foot by mis-assigning the datatype). In the meantime, you should be
able to test this by flipping 'allow_datatype_change' in interval.py
to True.
Thoughts?
Thanks,
Dan
On Jan 27, 2016, at 3:38 PM, Lance Parsons <[email protected]
<mailto:[email protected]>> wrote:
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_type,
u'Bed12', please verify.", u'files_metadata': [u"An invalid option
was selected for file_type, u'Bed12', please verify."]}}}
2. I see that Bed12 is in the datatypes_conf.sample file. Is there a
way to add a converter for that datatype? Perhaps something
like:https://wiki.galaxyproject.org/ToolShedDatatypesFeatures#Including_datatype_converters_and_display_applications?
My concern is that since it already exists, I wouldn't be able to add
a converter. Also, the sniffer doesn't seem to work (it just finds
the files as "bed", thus my desire to specify ftype in tests).
Thanks,
Lance
Daniel Blankenberg wrote:
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 of bedstrict. They can of course be consumed
or created by any sort of tool. Please let us know if we can provide
additional information.
Thanks for using Galaxy,
Dan
On Jan 14, 2016, at 4:26 PM, Lance Parsons<[email protected]>
wrote:
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 part of the core galaxy (which would allow multiple tools to
share the same data type definitions) or making it part of a
toolshed tool (which I'm not sure how to do)? BTW, I'm thinking
about RSeQC at the moment, but I know other tools use/require this
format.
--
Lance Parsons - Scientific Programmer
Carl C. Icahn Laboratory - Room 141 (Temporary)
Lewis-Sigler Institute for Integrative Genomics
Princeton University
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Daniel Blankenberg <mailto:[email protected]>
January 25, 2016 at 9:47 AM
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 of bedstrict. They can of course be consumed
or created by any sort of tool. Please let us know if we can provide
additional information.
Thanks for using Galaxy,
Dan
Lance Parsons <mailto:[email protected]>
January 14, 2016 at 4:26 PM
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
part of the core galaxy (which would allow multiple tools to share
the same data type definitions) or making it part of a toolshed tool
(which I'm not sure how to do)? BTW, I'm thinking about RSeQC at the
moment, but I know other tools use/require this format.
--
Lance Parsons - Scientific Programmer
Carl C. Icahn Laboratory - Room 141 (Temporary)
Lewis-Sigler Institute for Integrative Genomics
Princeton University
--
Lance Parsons - Scientific Programmer
Carl C. Icahn Laboratory - Room 141 (Temporary)
Lewis-Sigler Institute for Integrative Genomics
Princeton University
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at:
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