How to run TCl to do operation in Quartus II?

To be honest, there are almost too many ways to do Tcl scripting with Quartus.

You can do:

quartus_sh -t <script>

This runs outside of the project, so you need to open and close the project if you're making assignments to it. The nice thing with this is it allows you to control Quartus projects. For example, I made my own seed sweeper in this manner, before Design Space Explorer was around. There are other modules besides quartus_sh. There's quartus_cdb to run ECOs. quartus_sta can do timing analysis scripts.

In Quartus you can go to Edit -> Tcl Console, and then source Tcl files from there.

What is it you're trying to do?

And don't forget the invaluable command for scripting:

quartus_sh --qhelp