The duration of a single plasma discharge in next generation of fusion experiments will be much longer than in the present devices. Storing all raw data acquired in each discharge will be more difficult and the high rates achieved by the new digitizers are already contributing to storage overload. The problem can be mitigated by Real Time (RT) analysis and compression, using devices such as FPGAs capable to transfer and process data on the fly. To ensure a correct RT analysis, the FPGA algorithm must be adapted to the signal to be acquired. It is important to know in advance the signal attributes as minor changes in signal shape may require significant algorithm modifications. For that reason, the availability of more than one RT algorithm is important, especially during commissioning of new sub-systems and during campaigns with relevant changes in diagnostic conditions. This paper presents an implementation using two RT algorithms processing simultaneously, developed for the gamma-ray and hard X-ray diagnostics of the Joint European Torus (JET). Both algorithms perform pulse height analysis with pile-up rejection. The first algorithm is suitable for Gaussian shaped pulses and the second is suitable for exponential signals. The algorithms are selectable by the user, during discharge configuration. Tests made at JET with radioactive sources are presented.