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 ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:

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