Can I pass command line arguments to basex while executing a xquery script?

You may run a script with the "run" command and prefix it with other commands. An example:

basex -c "open ...; ...; run yourquery.xq"

With 7.1 and the latest snapshot, you can use an arbitrary number of commands, query files etc:

basex -c "open...." yourquery.xq

Hope this helps, Christian