Hi,
Firstly I would like to say that masters in physics is a really good course and your future is bright. Speaking about minimum eligibility, 50% aggregate would mean 50% in overall BSc honours, but some universities do make it compulsory to get 50% in each subject specially physics chemistry and maths. So if you have a doubt I would recommend you to mail the university itself. That will clear your doubt first hand.
All the best