Assaf,

Thanks for the very helpful information. We largely sync our tool wrappers to 
the tool version used on our public server. We're currently running v1.0.1 of 
Cufflinks on main; hence, as you discovered, the wrappers are compatible with 
that version of Cufflinks but (sadly) incompatible with newer versions.

If you modify the Cufflinks/compare/diff wrappers to be compatible with 
1.0.2/3, please either put them in the toolshed or send them to me and I'll 
incorporate them into the Galaxy code base.

Thanks,
J.

On Jun 6, 2011, at 2:42 PM, Assaf Gordon wrote:

> Hi,
> 
> It seems the cuffcompare XML wrapper expects a file named "cc_output" to 
> contain the "transcript accuracy" report.
> I guess it worked with versions 0.9.3 and 1.0.1, but at least in version 
> 1.0.2, this file is now named "cc_output.stats", and the "transcript 
> accuracy" file is empty.
> 
> so the XML wrapper is compatible with 1.0.1 but not really with 1.0.2/3 
> (Unless I missed something in the XML/python/cuffcompare execution chain).
> 
> 
> Also,
> Notice that starting version 1.0.2 they've added an option to normalize by 
> either total number of reads or by number of reads that matched the given GTF 
> file.
> To make matters worse, "cufflinks" defaults to normalizing to total reads, 
> and "cuffdiff" defaults to normalizing by GTF-matching reads.
> The options are called "--total-hits-norm" and "--compatible-hits-norm".
> 
> There's no way for users to specify either of those in Galaxy, so running 
> cufflinks/cuffdiff might give unexpected results (not that there are any 
> "expected" results, but still...)
> 
> Just something to think about when you work on the next version of cufflinks 
> wrappers.
> 
> -gordon
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