Yes, scientists use the Tuxedo suite (available on the public Main Galaxy http://usegalaxy.org) for bacterial genomes, forums like biostars.org and seqanswers.com will have more discussion about the processing, as will publications in your field. Alternate tools/packages have also been wrapped. All are available in the Tool Shed, for use in a cloud or local Galaxy.
Other public Galaxy's tools sets may also be of interest (may or may not be in the Tool Shed, and many offer public accounts/processing).
And here is a blog forum that is more specific to the task, to help provide some leads.
I just saw Bjoern's reply (to the original sub-post) and second this - really any tool that you want to use can be added to Galaxy and used. Galaxy is used for more than bioinformatics, even.
Best, Jen, Galaxy team