Bean and tomato stew

I am trying to use things up. I don't eat cheese, but S does, and I couldn't let him throw away a perfectly good parmesan rind. This also used up some beans and red wine that had been waiting for their moment for too long. And it's a good combination: beans and tomato and herbs and lush, rich sauce.

~2 tbsp olive oil
1 onion, peeled and chopped
2-3 cloves garlic, peeled and chopped
1 tin tomatoes
~2 tbsp tomato puree
1 parmesan cheese rind
1 tin lima beans
~1 1/2 cups white beans (cooked and frozen)
~1/2 cup red wine
1-2 tsp dried oregano
1-2 tsp dried basil
1-2 tsp dried thyme
pinch of dried red chilli flakes
2 bay leaves
1-2 tsp dark soy sauce
salt+pepper

Heat olive oil in a large saucepan, add onion and garlic, cover and cook until softened. Add the remaining ingredients (except salt, pepper and soy sauce), cover and cook for at least 45 min, before turning off the heat, tasting for seasoning (salt, pepper and soy sauce) and letting sit for another half an hour. Remove the cheese rind and bay leaves and reheat to serve. Good with bread or pasta or polenta.