1.) Please see attached. 2.) So I did this for tophat and cufflinks. This would be useful for cuffcompare. Cuffdiff uses the gtf files output from cufflinks and not reference gtf files.
Following a conversation we had with James, I plan on editing the xml scripts to pull the genome attributes from a previous step as opposed to having to set them. From: Jeremy Goecks [mailto:jeremy.goe...@emory.edu] Sent: Wednesday, October 12, 2011 1:22 PM To: Chorny, Ilya Cc: email@example.com Subject: Re: Some changes to tophat and cufflinks wrappers for indexing loc files 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. Ilya, This looks like a good start. A couple questions: (1) Do you have a sample GTF indices file similar to e.g. bowtie_indices.loc.sample ? (2) Would it be useful to provide GTF index files in Cuffcompare, Cuffdiff, and Tophat as well? Thanks, J.