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I suggest that you use ALTCLKCTRL blocks to mux the clocks, if you aren't already doing so.
As far as constraints go, the mux's output signal isn't handled as if it were a separate clock. Thus, set_clock_groups only takes the mux's inputs and the rest is handled automatically.
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I could see that Quartus has added one CLKCTRL cell after the clock mux before pushing into Global Clock Tree and hence I can get the pin "clkctrl|outclk" using [get_pins -hierarchical *clkctrl|outclk]. But again "set_clock_groups" fails saying that the return value of the "get_pins" is not of type {clk}.
I shall look into ALTCLKCTRL further and shall update this thread with the results.
Regards
Manish