BUG: Pass file path to convert_biom_to_table

This function did not deal well with file like objects now that HDF5 is
a supported format, internally changing convert_biom_to_table to use
biom.load_table fixes this problem.

Fix #1598
Merge pull request #1599 from ElDeveloper/supervised-learning-hdf5

BUG: Pass file path to convert_biom_to_table