It turned out simple. At least for my NTuples. I write a python script where it reads the branches from the root tree and writes them into the NumPy array. Then I created the hdf file and wrote these NumPy arrays to the hdf file.
It worked for me. In case that if someone is particularly interested, I can distribute my code.
An alternative approach that has worked for others involves writing a Python script to read the branches from the ROOT tree and write them into NumPy arrays. Then, you can create an HDF5 file and write these NumPy arrays to it. This method has been successful for some users