Output CLOCK signal to GPIO pin of CYCLONE IV E
What's the bandwidth on your scope?  If it's not significantly greater than 50 MHz (say, 500 MHz or more), the scope's bandwidth limit will turn your square wave into a sine wave.  This is because a square wave consists of a series of odd frequency harmonics...in this case 50 Mhz, 150 Mhz, 250 MHz, etc.  So if you have, say, a 100 MHz scope, you will miss all of the frequency components except the fundamental at 50 MHz, and you'll get a very nice sine wave even though you actually have a square wave with very sharp edges and lots of high frequency harmonics.  If you use a 500 MHz scope, then you'll get 50, 150, 250, 350, and 450 MHz which will result in a nice square wave.  And using mile long jumper wires like that will certainly not help with signal integrity.