Try using the
gtf version of the annotation instead. This tool does not accept
gff3 formatted annotation.
This can get a bit confusing since the tool form states
gff as an input, and will accept files with that datatype assigned. This is because many data sources provide
gff+gft hybrid data – and the only difference between those two is the last column (attributes). Some also release
gff3 data that is given a
gff datatype (including this source: https://www.arabidopsis.org). The
gff3 format is structured and labeled much differently than
gff or gtf.
These data are incredibly difficult to automatically assign a datatype to, because there can be so much variation from sources. Custom header lines can interfere, blank lines, etc. It is usually a good idea to check the format yourself once in Galaxy to confirm the actual type. Sometimes headers need to be removed in
gtf datasets before certain tools will consume them properly.
This FAQ explains each, how they are similar/different, and reformatting/transformation tips.