quartus_fit switches equivalent for quartus fit QSF commands

It is not recommended to run all your commands from quartus_fit. A few things were added that are commonly used, and really seed is probably the only common one. Everything else should be stored in your .qsf. That being said, two options:

1) There is a generic --set option that allows you to put in your own values, i.e. .qsf settings directly.

2) Rather than passing arguments via quartus_fit, have a separate .tcl file you call with quartus_sh --t filename.tcl

project_open <project_name>

set_global_assignment -name WEAK_PULL_UP_RESISTOR [ON | OFF]

set_global_assignment -name AUTO_MERGE_PLLS [ON | OFF]

project_close

This puts them in the .qsf and they will be used by the fitter.