This started as a question, and I think ended up with an answer. Figured I would post anyway, mainly to document my experience, maybe it is handy for the developers or another user.
I am using a local docker version of OMERO CLI to upload to a remote OMERO server.
docker run --rm -v /media:/tmp --entrypoint=/opt/omero/server/OMERO.server/bin/omero openmicroscopy/omero-server -s example.com -u exampleuser upload /tmp/file.tif
After running the command I got the message:
OriginalFile:159 This module is deprecated as of OMERO 5.5.0. Use the module available from https://pypi.org/project/omero-upload/ instead.
I then realised that I should follow the instructions here:
A command similar to:
docker run --rm -v /media:/tmp --entrypoint=/opt/omero/server/OMERO.server/bin/omero -s example.com -u exampleuser -g exampleusergroup import -d 4 /tmp/file.tif
I guess that marking the command as upload (deprecated) might be handy for new people to know that they need to look elsewhere, since it is at the top level of commands that you can see.