Hello Elihu, The tool was just recently upgraded to include these files. https://trello.com/c/FdUYdbIn The update will be available in the Tool Shed then updated on the main public server at (or possibly before) the next stable release. Other pending updates to the tool suite include adding these additional features. https://trello.com/c/lIdpOZ88 https://trello.com/c/U7nceKdj Good question! Sometimes the updates are because the tool itself changed, sometimes they are simply updates to add in more features as they are requested/needed. The Trello cards will usually note the history and any comments. Jen Galaxy team On 11/20/13 6:22 AM, Aranday Cortes, Elihu wrote:

Hi,

Cuffdiff in Galaxy produces "read_group_tracking" files. However, I wonder if these files are enough when using 'replicates=T' in cummeRbund or I also need "read_groups.info" and "run.info" files in myDir.

I've tried 'replicates(cuff)' with the 'read_group_tracking' files in my directory and I get back an empty set, means that cummerbund is not using replicates (or I'm doing something wrong!). At this time I don't see other option that run cuffdiff locally. At least you have any suggestion or advice about how I can get 'info.files' from Galaxy.

Any particular reason why Cuffdiff output files in Galaxy are not ALL the files described in the manual tool?

Thanks for you help.

Elihu

___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:

http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists, please use the interface at:

http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:

http://galaxyproject.org/search/mailinglists/

-- Jennifer Hillman-Jackson http://galaxyproject.org