If you use Freebayes to do the variant calling, realignment is performed by that tool during execution (a distinct realign step is not needed).
If using a different caller, try BamLeftAlign.
Please see the Galaxy variant analysis tutorials for the full details and example protocols: https://galaxyproject.org/learn/
Note: Avoid using GATK in Galaxy as all of those tool wrappers have been deprecated. New versions are under development but not quite available yet.
Thanks! Jen, Galaxy team