I think that most of the claims of a link between vaccines and autism are for the MMR vaccine. So maybe the whooping cough vaccine would be acceptable to your wife, if the autism link is her main objection.
The morality and health effects of vaccines are issues that my wife and I have struggled with, and I don’t know if we have come to the right conclusions or not, so I am not going to advise you for or against particular vaccines, or for or against vaccines in general. But please let me share some insight from my own struggles with this issue, that might be helpful in how you address the issue with your wife:
What I found the most frustrating as we tried to figure out which side (pro-vaccine or anti-vaccine) was right, was that both sides tended simply to dismiss the other side’s arguments as stupid or irrelevant or not worth taking the time to respond to. I found very few voices on either side of the debate that were willing to take a calm, measured approach to the other side’s arguments, and at least to acknowledge that those on the other side shared the same motivation of wanting what is best for the children. I found very few voices that would acknowledge that the other side does have at least some valid concerns, even if they disagree with the other side’s conclusions.
I found this dismissive attitude from both sides to be a major obstacle to reaching an informed decision on this topic. And I think that comments like “just because some hippies say it causes autism” do not represent a helpful and productive attitude to bring to discussions with your wife.
When I was investigating this issue several years ago, I did find one book that at least tries to present a somewhat balanced approach to the issue, and which might be useful for you and your wife to read:
Vaccinations: A Thoughtful Parent’s Guide: How to Make Safe, Sensible Decisions about the Risks, Benefits, and Alternatives by Aviva Jill Romm
This book comes down a bit more on the anti-vaccine side, but not entirely, and it at least gives a respectful treatment to the pro-vaccine point of view. It also contains descriptions of the symptoms and risks associated with diseases like measles, mumps, whooping cough, tetanus, etc. I am not necessarily endorsing the author’s conclusions; I am just saying that this book might be one book, along with others, that you and your wife could read to help you make an informed decision.
Finally, you also may want to consider the fact that some vaccines are made with aborted fetal tissue, and whether or not you should ask your doctor to order alternate vaccine versions that do not use aborted fetal tissue. While I don’t necessarily agree with everything on this site (and I am sure that you won’t either, given their current headline about autism), here is the web site where I have found the best information on this issue:
cogforlife.org/
In particular, see this page, which gives a detailed list of which vaccines use aborted fetal tissue, and which ones do not:
cogforlife.org/vaccineListOrigFormat.pdf
They also have a response from the Vatican on this issue:
cogforlife.org/vaticanresponse.pdf