There are several wrapped tools for rRNA analysis in the Tool Shed and any other tool that you need could be wrapped for Galaxy (if you have that resource available). These tools are for use in a local/cloud Galaxy and there are Public Galaxy instances that host tools for this analysis. Below is also a link for a tutorial linked to some of these tools. Other publications/protocols can be reviewed from any source and compared to the tools Galaxy has wrapped already.
Search using the keyword 'rRNA' to locate tools:
In particular, please see what the GVL offers in the form of tutorials and the related tools. This will help you to decide how to set up your own cloud Galaxy if you decide to use their wrapped tools:
Hopefully this helps to get you started, Jen, Galaxy team