Ok, that's good, since it looks like the deprecated Tophat tool is not working with a custom genome right now. HISAT2 or RNA STAR are good alternatives. STAR does use much more memory during processing, so if your job fails for that reason, try HISAT2.
HISAT2 does do spliced mapping. See this tutorial for an example: https://galaxyproject.org/tutorials/nt_rnaseq/#spliced-mapping-with-hisat
All tutorials: https://galaxyproject.org/learn/
Thanks! Jen, Galaxy team