Ok, this helps. That’s is an interesting usage and as far as I know, not the intended input. Create the collections first before using collection operations tools.
Collection tools may need a tune-up to prevent this from happening. I’ll run through your use-case and run it by the developers. I’ll link back a ticket if one is created. Thanks for reporting this and sending details to reproduce!
More Collection help
Beginning tutorial for creating a collection: https://galaxyproject.org/learn/
- Dataset collections - modern studies usually include many samples. Collection are designed to simplify complex, multi-sample analyses as shown in this tutorial.
With advanced functions covered in these tutorials: https://galaxyproject.github.io/training-material/
I sent you the link to the alternative RNA-seq tutorial that uses collections in this post, which hopefully helped: