Hi,
I have a two factor design dataset for deseq2: cancer vs. non cancer and the subject id’s.
I can manually in galaxy assign files to the two factors, but given that I have 29 subjects it is a lot of “clicking”. Can I upload a file with that information somehow?
many thanks, Martijn
Welcome!
One way to do this is to use your metadata file to add in group tags to your set of files contained in a dataset collection folder. That can all be done at once (by also providing the data URLs) or you can apply the group tags after the data is in Galaxy.
For an example with DESeq2, see: Hands-on: Group tags for complex experimental designs / Group tags for complex experimental designs / Using Galaxy and Managing your Data
More tutorials for batch processing → Using Galaxy and Managing your Data / Tutorial List
Please let us know if you have any questions about this! 
thanks for you answer Jenna!
I will try this