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I was wondering if there is a way to use the --user parameter of docker to have the containers creating files with the users I need to use and not root.
There are no special Plesk CLI or API methods to manage Docker. Use the docker command instead. It provides you with a full set of tools to configure and manage Docker including --user parameter.
I see, but is it Plesk that manages what containers startup automatically (via "Automatic start after system reboot" option) or does it use some external process manager?