Is your spouse's domicile Texas too? And is in Calif only to be with you? If so you qualify for MSRRA and Calif can't tax your spouse's wage income (CA employer shouldn't be withholding Calif taxes). Calif can only tax Spouse's share of intangible income (interest, dividends) and non-Calif source income.
If you don't have any those things then file a Calif nonresident Form 540NR, claiming 0 income as Calif source to get a full refund of the Calif tax erroneously withheld.
If qualified for MSRRA, Spouse should fill out Form 590 and give it to CA employer, checking the box for Nonmilitary Spouse of a Military Servicemember, to stop the Calif withholding. https://ftb.ca.gov/forms/2017/17_590.pdf
Also, see California's publication 1032, Tax Information for Military Personnel, here
https://www.ftb.ca.gov/forms/2016/16_1032.pdf
You can find your situation in example 8.
