You'll need to upload the fasta of the reference genome the GFF data is based on so it can be used as a "Custom Genome". Then use the Extract tool with your custom genome "from the history". The input GFF won't need a database assigned, but you could go further and create a Custom Build and assign that as the database.
Format and content are both very important. Please review the FAQs below to avoid problems. https://galaxyproject.org/support/#getting-inputs-right. Start with these two and use the others in that same section as needed.
- Preparing and using a Custom Reference Genome or Build
- Mismatched Chromosome identifiers (and how to avoid them)
Thanks! Jen, Galaxy team