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
___________________________________________________________
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:
http://galaxyproject.org/search/mailinglists/
