Forget #2, I got confused with something else. :)
From: galaxy-dev-boun...@lists.bx.psu.edu
[mailto:galaxy-dev-boun...@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: icho...@illumina.com<mailto:icho...@illumina.com>
Website: www.illumina.com<http://www.illumina.com>
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