[galaxy-user] Aligning against Multiple Reference Sequences

Are there any tools in Galaxy to align short reads against multiple reference sequences?

I have a dozen microbial genomes sequenced for which there are 2 reference genomes already sequenced. We have tried aligning each of these individually against either of the reference genomes - some align better against the first reference genome, some align better against the second reference genome. Ideally though I would like to be able to align against both at the same time. Is this possible?

I have found a tool called GenomeMapper and hints of 2 other tools in development that do something like this, but nothing for Galaxy yet.

How do others proceed with this type of problem? Workflows appreciated! :)

-John