The genome dataset probably needs to have the datatype
fasta assigned. Then when selecting the genome on the tool form, choose the option to pick one from the history (instead of a built-in index).
The annotation dataset sounds like it already has the
gff3 datatype assigned so is appearing in the appropriate form locations.
Specifically, see the help in this section for how-to: https://galaxyproject.org/support/#getting-inputs-right
Tutorials, including those for RNA-seq: https://galaxyproject.org/learn/
Thanks! Jen, Galaxy team