The fasta reference transcriptome should have the datatype "fasta" assigned for the tool to recognize the input.
Here is help for correct fasta formatting for datasets used as Custom reference genomes/transcriptomes. Many mapping tools are not picky about the format, yet many downstream tools are. It is generally a good idea to ensure correct formatting as part of the prep stages before starting any analysis that uses a custom genome/transcriptome.
- CGs: https://galaxyproject.org/learn/custom-genomes/
- Other format help links: https://galaxyproject.org/support/#getting-inputs-right-
We hope this helps! Jen, Galaxy team