To assemble all the data together in one result, use the tool Concatenate to merge the replicates. Do this once for the forward reads and once for the reverse reads.
If a collection is used, then a separate assembly will be created for each pair in the collection.
Note: We have had some problems with this tool recently and when I just tested Unicycler with a collection input, the jobs failed. Single paired inputs worked fine this morning but the jobs are queueing a bit longer again now.
Why the queue is taking longer is not clear yet. Updates will be posted to this thread: https://biostar.usegalaxy.org/p/26313/
Why collection inputs fail is also not clear yet, but a ticket tracking the issue can be followed here for updates: https://github.com/galaxyproject/usegalaxy-playbook/issues/82.
Thanks! Jen, Galaxy team