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PORTLAND, Ore. — Natural grocer Whole Foods filed a federal lawsuit Monday against the Federal Trade Commission, claiming the regulator violated its due-process rights in a dispute over its acquisition of rival Wild Oats.

Whole Foods Market bought Wild Oats Markets of Boulder in 2007 for $565 million. Since then, the deal has been embroiled in an antitrust challenge that has Austin, Texas-based Whole Foods’ biggest acquisition in legal limbo.

The FTC thought the deal could create a natural-foods monopoly, but federal judges determined the acquisition could move forward.

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