Once you locate a publication/protocol that you want to follow and know the target tools, these are the options for doing the analysis within Galaxy:
Locate tools on the Main Galaxy instance under the tool group Metagenomic Analysis.
Other public Galaxy instances host some the same plus alternate tools. Search for "metagenomics" here: PublicGalaxyServers
Nearly any other tool could be wrapped for Galaxy, if you do not find the ones are you looking for. Add Tool Tutorial
Thanks, Jen, Galaxy team