There is no official support of converting Arduino code to Nios II C code. The longest way would be to re-write the example you use in Arduino to a bare-metal code for Nios II.
Arduino uses special functions of C language which is not supported in Nios II. the code that will be used to run the Arduino needs to be re-written in a plain C format to be compatible with Nios II. If there are libraries behind that Arduino code, you can use them directly with Nios II. However, this can be easily done if your libraries are written in C, if they are written in C++, you might find some challenges in handling them for Nios II since C++ requires large amount of memory to run on Nios II.
Hope this might help.