If your organism is not already annotated in tappAS, you can use IsoAnnotLite to re-format your GTF file and make a tappAS-compatible GFF3 file. However, bear in mind that this file will not contain functional labels, and therefore that you’ll only be able to run tappAS Differential Module.
While any organism can be potentially annotated at the functional level, adding functional labels is quite complex. At the moment, we are working on having a robust pipeline for de novo transcriptome annotation, unfortunately, it is not ready for public use yet. Of note, IsoAnnotLite contains an option to positionally transfer functional labels from an already-annotated GFF3 file, but cross-species usage is very likely to fail.