I assume that the money shows up in Box 12 of your W-2, coded "W."
If that's the case then you can't take a deduction for the contribution because the money that was deposited in the HSA - an account that you own and control - was never taxed in the first place. Box 12 money coded "W" is money that you earned from your salary or wage, but it's NOT included in Box 1 of the W-2, so it will never be taxed.
You can't contribute pre-tax money AND take a deduction for that money; that would be double dipping.
On the other had if you took money out of your checking account - after tax money - and made a contribution to an HSA that contribution would count as a deduction.