Oh sure, we keep everything that was once available for reproducibility reasons! Very important! We don’t want to break anyone’s workflow! Either an actual workflow or just how you are using the tools.
The prior versions of the SPAdes tool can be navigated with the Versions menu at the top of the tool form. If you were using individual datasets for a pair before, one of these was likely what you were using.
The most recent with this type of input was 3.15.5+galaxy3. → FAQ: Changing the tool version
And, I’ll just add that you can Upload data directly into a collection, too. This is built into the Upload tool now and routes directly to the collection builder. Most is automatic – just name the collection on the next screen. Please ask if you have a question about it! Creating a collection in the history is just another route but most people will load data this way at the start.
Collections are how to process a lot of data but being able to jump in for exploratory work is important too! We do want feedback about this .. so if you run into any problems or have suggestions, more comments here are great. Me and others helping are also core project developers so you are speaking to the right people! 