Yes, the issue was with the collection identifiers. The last test in the shared history is still waiting to run but I’m expecting it to be successful, or to at least present with a different error (content, not format).
I’ve decided to make a request to correct the tool wrapper, if possible. → Bug: PanTA requires element identifiers ending in "gff". Conflicts with new default "Auto Build List" defaults (strips extensions) · Issue #7349 · galaxyproject/tools-iuc · GitHub
This topic has some advice about a similar issue (spaces in the identifiers) → Panaroo error - missing dependancies? - #6 by Nanobes
Workaround for end-users
- Name your collection’s element identifers like this:
sample.gff
- all one term
- no spaces
- ending with a
.gff
- Not sure how to check your element identifiers or modify them? See this topic at the forum Panaroo error - missing dependancies? - #6 by Nanobes and search our tutorials with the keyword “collection” for more!
The exact process will be different for everyone, but the instructions above (extracting and directly applying new identifiers for those who prefer text manipulation utilities) and the examples in the shared history above (using another method) can get you started.
Collection 4331 with the rerun icon to bring up the Apply Rules tool
Example parsing. The List Identifiers is the core bit to make sure to assign. Other metadata can be broken out into tags if wanted.
GTN Tutorials → Using Galaxy and Managing your Data / Tutorial List
Hope this helps but please let us know if it actually does! 
Once you get a copy of the testing history, let me know and I’ll purge it.