In this case, there's not much of a difference in meaning. However, this doesn't mean they are always interchangeable. "Was going to" indicates that plans had been made to do something; "Wanted to" does not necessarily mean that. For example, you could say, "I wanted to go to John's beach house this weekend, but he didn't invite me." It would sound a little awkward to say, "I was going to go...." since it is not the speaker's place to make plans about someone else's house.

"Was going to" implies an intention, but not necessarily a desire to call. "Wanted to" means you I had a desire to call.