Pick one that fits your data (Transcriptome, Whole Genome, etc). If the tool produces an alternate format (for example, if FASTQ is produced, convert to BAM format using existing wrapped tools such as those from Picard). Each 3rd party tool will have documentation about the data types appropriate for use. Reviewing publications that involve your specific datatype can also help guide you to the assembly tools to explore. If needed, one can also wrap pretty much any other tool for Galaxy, if programming resource is available.
Thanks, Jen, Galaxy team