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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Daniel Blankenberg

 

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

 

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