sim_to_train.py allow organism pseudonyms, multiple -b options and custom filename

[laylagerami]

Reference to this issue with sim_to_train.py
Need to put organism in exactly and with quotes e.g. --organism 'Homo sapiens' not 'homo'
Also need to put one option for -b e.g. -b 1 not 0.1,1,10,100
You also cannot specify your own custom filename

This is confusing because in predict.py you can use organism pseudonyms, have multiple -b options and have a custom filename, thus we should change the script to allow this.