Is it possible to have a reference genome added for Cryptococcus neoformans H99?
The genome assembly and annotation of strain H99 is available in Genbank under project accession PRJNA411 and also available at FungiDb.
For most tools, using a Custom Genome Build is how to use a reference genome that isn’t indexed on the server. This recent Q&A has the details → Reference Genome - #2 by jennaj
It looks like the data source has both the reference genome (fasta) and reference annotation (GFF) data, which is exactly what you will need to work with the genome in Galaxy. Getting both at the same time is strongly recommended.
Hope this helps! 
Sure, could you provide both formats?