Wells was Selected by the San Diego Padres in the 31st round of the 2002 Major League Baseball Draft, signed by San Diego Padres scout Jay Darnell in 2003. That year, Wells was assigned to the Short-Season A Eugene Emeralds. He had a record of 4-6 with a 2.75 ERA. The ERA was good enough for seventh lowest among Northwest League starters.\n', '

In 2004 Wells was sent up to the Single-A Fort Wayne Wizards. He compiled a 4-6 record with 4.09 ERA in 14 starts. This soon earned him a promotion to the Advanced-A Lake Elsinore Storm there he had a record of 4-6 with a 4.52 ERA in 12 starts.\n', '

The Padres decided to keep Wells at the Advanced-A level but he soon found himself a promotion to the Double-A Mobile BayBears in 2005. He went 13-8 with a 3.68 ERA in a combined 163​1⁄3 innings between the two clubs, tied for the lead among Padres\' farmhands in wins, while his ERA ranked fourth. Wells captured the California League ERA title and was named the league\'s Pitcher of the Year. Wells was named the Padres Minor League Pitcher of the Year at the club\'s annual organization postseason Awards Dinner on November 3.\n', '

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