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Description
Thanks a lot @jmchilton for fixing the issue: #20270
The problem is resolved, and all deferred files are used in the tool. (I tried it here: https://usegalaxy.eu/u/nilchia/h/test-differed-data [data 21: Concatenated datasets
])
However, there is still another issue with deferred data. The file name (element_identifier) is not correct. It is set to ("Unnamed dataset") for all of them.
In the same history above if you click on the info and check the output, you can see this:
Concatenating files:
Unnamed dataset...Done
Unnamed dataset...Done
Unnamed dataset...Done
Unnamed dataset...Done
Unnamed dataset...Done
It is problematic for tools such as VPT when the files are being symlinked and the tool checks the file names.
The deferred file in the history panel has the correct name:

Thanks a lot for fixing the issue!
ping: @bgruening
Galaxy Version and/or server at which you observed the bug
Galaxy Version: 25.0
Server: EU
Browser and Operating System
Operating System: Linux
Browser: Firefox
To Reproduce
Steps to reproduce the behavior:
- Upload some data as deferred
- Use them in a tool
- Check the job command; the data name is not correct
Expected behavior
The tool should detect the file name correctly.