I have been using cufflinks on Galaxy Main.  I have downloaded the files 
generated but they do not correspond to the file names expected by cummeRbund.  

For example:
cummeRbund expects 4 tracking files (e.g isoforms.fpkm_tracking) , 4 .diff 
files (e.g isoform_exp.diff).  

Here is a trimmed version of the output I download, grouped by what Im guessing 
is the tracking, diff and usage files:


TRACKING
...Galaxy109_transcript_FPKM_tracking.tabular
...Galaxy107_gene_FPKM_tracking.tabular
...Galaxy105_TSS_groups_FPKM_tracking.tabular
...Galaxy103_CDS_FPKM_tracking.tabular


.DIFF

...Galaxy108_transcript_differential_expression_testing.tabular
...Galaxy106_gene_differential_expression_testing.tabular

...Galaxy102_CDS_FPKM_differential_expression_testing.tabular

USAGE
...Galaxy99_splicing_differential_expression_testing.tabular

...Galaxy100_promoters_differential_expression_testing.tabular

...Galaxy101_CDS_overloading_differential_expression_testing.tabular



Given that cummeRbund is a common next step in the workflow, is there an option 
to save the output in the expected format, perhaps with a galaxy history number 
prepend?  I'm not sure which files are to be renamed and to what name and it 
seems that one file is missing.

If there were a cummeRbund implementation on Main it probably wouldn't matter 
as much but until that happens, I (and i'm guessing other newcomers) would 
appreciate the help!

Thanks,

mike
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