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 <lpars...@princeton.edu> 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<lpars...@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
>>> 
>>> ___________________________________________________________
>>> Please keep all replies on the list by using "reply all"
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>>> 
>>> To search Galaxy mailing lists use the unified search at:
>>> http://galaxyproject.org/search/mailinglists/
>> 
> 
> 
>> 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
> 

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