Any MAF can be used in Galaxy with the tools, but only a few are included as build-it reference data on the public Main Galaxy instance at http://usegalaxy.org. These do not include mm10 at this time.
If you are working on a local/cloud Galaxy, a MAF dataset can be installed as a build-in reference file. See our admin instructions and model after the currently included MAFs from the rsync server. Or, if just want to use it on a public site, load it into your history and use it from there.
The mm10 MAF at UCSC is a good choice: http://genome.ucsc.edu/ --> review track in mm10 browser ("Conservation") and obtain the files from their downloads area.
Adding this to Main is worth considering. I'll follow up on this and create a ticket/post it back if a yes.
Thanks, Jen, Galaxy team