I personally do not know of any free tool that would achieve what you are looking for. The closest thing would be to use a “slice and chop” company that would take your designs and slice them up for you at a price though.
There is a great “blank” wordpress theme out there that I use on all of my projects. It has all of the files you need for a theme, with most (if not all) of the queries that you need. All you have to do is pretty much style it.
However, the WordPress Codex is a great resource for learning all the nuts and bolts of wordpress. I know it has been a life saver to me over the years.