Mappers that permit long-read inputs would be appropriate such as: Blast, BLAT, etc.
To see all mappers already wrapped for Galaxy, review the category "Next Gen Mappers" in the Tool Shed.
If the tool you wish to use is not wrapped for Galaxy yet, it could be. There are some specialize mappers for circular genomes available in the wider bioinformatic community, some proprietary, but I don't believe any have been wrapped for Galaxy yet (but we may still get more replies).
Also see this prior question at the main Biostars site: https://www.biostars.org/p/10081/
Best, Jen, Galaxy team