Thanks Ilya. This is definitely something we plan to include in Galaxy, but I'd 
been holding off looking into it because of the our planned changes to the tool 
data tables. Once these enhancements are in place, I'll take a look at these 
patches and ensure that they are compatible with these changes.


On Sep 30, 2011, at 6:20 PM, Chorny, Ilya wrote:

> I made some changes to the cufflinks and tophat wrapper to pull gtf files 
> from an indexed loc file as  opposed to from history. The diff’s are 
> attached. I made it an optional feature. Please let me know if this makes its 
> way into galaxy-central.
> Best,
> Ilya
> Ilya Chorny Ph.D.
> Bioinformatics Scientist I
> Illumina, Inc.
> 9885 Towne Centre Drive
> San Diego, CA 92121
> Work: 858.202.4582
> Email:
> Website:
> <cufflinks_wrapper.xml.diff><tophat_wrapper.xml.diff>

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