Amounts shown on your W-2 in box 12 with code W can be your contributions from your paycheck, or contributions made by your employer. There is no distinction between the two values if you both contributed. Either way, the contribution was made through your company's payroll system.
When the money was taken out of your paycheck for deposit into your Health Savings Account (HSA), it was done with pre-tax money. Therefore, you have already received the tax benefit from making that contribution.
If you were to make an additional contribution to the HSA outside of the payroll deduction, then that would be after-tax funds and the amount would be shown on your tax return as a deduction.
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