In Quartus® II software versions 13.0sp1 and earlier, you must specify the C counter value (cnt_sel) based on the physical counter index, to select the counter to be phase shifted. The physical counter index information is available in the Clock Networks and PLLs chapter of Arria V, Cyclone V and Stratix V Device Handbooks.
In Quartus II software version 13.1 and later, users can specify the C counter value (cnt_sel) based on the logical counter index. The logical counter index maps to the output clocks (outclk0, outclk1…) number in the Altera PLL megafunction.
For Quartus II software versions 13.0sp1 and earlier, specify the value of C counter value (cnt_sel) with physical counter index.
For Quartus II software versions 13.1 and later, specify the value of C counter value (cnt_sel) with the logical counter index.