Honestly, it depends on the intonation of the question. Answers 1 and 2 only make sense if it was a yes / no question, but in real life, it would probably be an either / or question, so we would not answer “Yes”; we would answer “I wrote it with a pen.” That’s number 3 (4 would also work, I suppose), so I agree with Ridvan Demir, and disagree with “Teacher Mac”. Imagine the waitress asks you if you'd like a soup or salad. Do you say "yes", or do you say "soup please"? Emu, I'm going to suggest that the question is not really useful for learning English.