House Training an Abused Dog?

I adopted a dog who was severely abused and she is kind of potty trained. She'll walk from door to door when she needs to go out, but she'll make you take her out two or three times before she'll go or she'll end up just going in the house.

So I guess my question is how do I get her to not go in the house and what do I do when she does go in the house? She cowers a lot and won't even let you put your hands on her back without her freaking out because she thinks you're going to hit her. We cannot get her in her crate. We've tried and she just won't do it. She gets so freaked out and looks terrified and won't let you go near her for a while. So how can I teach her how to speak when she needs to go outside and what do I do when she goes inside?