Forget #2, I got confused with something else. :) From: galaxy-dev-bounces@lists.bx.psu.edu [mailto:galaxy-dev-bounces@lists.bx.psu.edu] On Behalf Of Chorny, Ilya Sent: Wednesday, September 28, 2011 4:06 PM To: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] GTF files in Cufflinks and Tophat Jeremy, 1.) Would you be interested in a feature in which the gtf files could be "locally cached" instead of only "from history"? 2.) Would you be interested in a feature in which cufflinks choses the genome in a fashion similar to how samtools know which which genome to use? i.e.: <when value="cached"> <param name="input1" type="data" format="sam" metadata_name="dbkey" label="SAM File to Convert"> <validator type="unspecified_build" /> <validator type="dataset_metadata_in_file" filename="sam_fa_indices.loc" metadata_name="dbkey" metadata_column="1" message="Sequences are not currently available for the specified build." line_startswith="index" /> </param> </when> I am happy on working on these changes if they will be put 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: ichorny@illumina.com<mailto:ichorny@illumina.com> Website: www.illumina.com<http://www.illumina.com>