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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