All contributions made through payroll deductions are listed as code W, employer contributions, regardless of whether the contribution came from the employer or the employee.
It's treated as coming "from employment." and it's excluded from your wages in box 1(pre-tax). You can't deduct the $2500 that your wife contributed, as it's already been excluded from her income.
If she contributed an additional amount (after tax) on her own, you would enter that as an additional contribution.
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