Designing a peripheral for soft core CPU
You may want to implement this as a custom instruction rather than mem-mapped peripheral. Get started by reading the NIOS II Custom Instruction Guide. You probably want to implement a 'Multicycle' instruction so that you can take a few cycles to calculate the DES  values. 

The guide explains how the instruction mnemonics trigger your hardware. The result is multiplexed together with the ALU output and directed to the register file. The example in the guide is a CRC generator, so somewhat similar architecturally.