You probably need to assign the datatype and/or database to the inputs.
Also, be sure to double check the GFF/GTF format - this tool has specific content/format requirements described on the tool form - please be aware that the tool does not accept GFF3 formatted annotation. The attributes gene_id and transcript_id must be present in the 9th field. If a custom genome/build is used, that must also be formatted correctly.
FAQs that will help with the above: https://galaxyproject.org/support/#troubleshooting.
Start with these:
- The tool I'm using does not recognize any input datasets. Why?
- How do I find, adjust, and/or correct metadata?
- Common datatypes explained
- Preparing and using a Custom Reference Genome or Build
- Mismatched Chromosome identifiers (and how to avoid them)
If the job later fails, there is likely an input format/content problem. This FAQ has summaries that link to other more specific FAQ help, including those listed above:
- My job ended with an error. What can I do?
Galaxy Tutorials covering tool/workflow usage help within a scientific context:
Thanks! Jen, Galaxy team