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
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<lparsons@princeton.edu> 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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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
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.
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
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.