When I try and added the M117-collection as a paired collection it doesn’t allow me even though the file format is correct
Welcome @Katlego_Hodgson
There are several input choices for this tool. If your data is in a paired-end collection, then this is the choice from the pull-down menu.
This is the tutorial it seems that you are following, yes? → Hands-on: Using dataset collections / Using dataset collections / Using Galaxy and Managing your Data
If you would like to capture some screenshots or generate a shared history link, we can try to help you more. Where to find those details are included here.
Hope you have solved this but if not we can follow up more here! 