Hi @aaak
Yes, this is a known limitation is related to the web browser behavior. We are still working on a solution. I’m glad you asked since I don’t think it has been discussed here yet and I’m sure it is frustrating for people!
We agree about all of the clicking being tedious. Using collection folders is the “Galaxy way” to avoid this. It sounds like you already know how to use collections, so I’m going to use this opportunity to explain for others reading who happen to find this topic!
What to do
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Put all of your files of the same type into a List collection folder.
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Choose the collection input instead.
This is a little FAQ and video that shows how to do create a collection quickly!
When working with so many samples, using name tags will likely be helpful to track samples through tools.
Hands-on: Name tags for following complex histories / Name tags for following complex histories / Using Galaxy and Managing your Data - > How to add trackable samples tags for datasets (“elements”) inside of collections
Backing up, if you start off with your reads inside a collection, you can run all of the downstream tools on multiple samples all at the same time. Or, you can add data into a collection later. This is another example video quickly showing how processing with collections works.
More about using collection folders in Galaxy.
GTN Materials Search (query=collection)
Please give this a try and let us know if it works or not! Follow up questions are welcome. 