TurboTax Deluxe will allow you to prepare your tax return based upon the information in your question.
Your wife will use Schedule C Profit or Business Loss to report her income and expenses. The home office deduction will be taken using Form 8929.
The expense of adding the 100 sq ft to your house is a capital improvement and will be added to your adjusted cost basis it is not depreciated.
A capital improvement is the addition of a permanent structural change or the restoration of some aspect of a property that will either enhance the property's overall value, increase its useful life or adapt it to new uses.
The cost of the flooring and finishing is not generally considered to be a capital improvement. It is considered as normal repair and maintenance and is not a deductible expense.