There are tools in the group Text Manipulation that can be used to add on a "chr" to the chromosome names. However, this will not always make the file match up with a UCSC-sourced reference genome without other changes. So if you decide to do this, be sure to double check the chromosome names before using the data with other tools or before attempting to visualize the data in the UCSC Browser.
Mapping against the correct target genome is a better way to fix the mismatch problem (map against the UCSC-sourced genome instead of the Ensembl-sourced genome). Using the same exact reference genome for all steps in an analysis ensures that data mismatch errors (or incomplete results) do not come up.
Thanks! Jen, Galaxy team