Hi all,

Jeremy Goecks wrote, On 06/07/2011 01:25 PM:
> 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.

We are actually working on customized version of those tools, with parameters 
which better suit our needs, I'm happy to share.
They are far from stable, so no tool-shed yet.

The XML's are here:

They use Cufflinks 1.0.3, but also require a small patch to Galaxy (included in 
the tarball), to add our "$input.tag" labeling hack.
Without this patch, you'll need to modify the <output> labels and the "--label" 
parameter of cuffdiff (with this patch, it calculates the labels automatically).

See the working interface go here:

Comments are always welcomed,

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