Police say the 36-year-old worker got into the argument with three men who entered the Orchard Street shop just after 10:30 p.m. and started taking items.
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They reportedly stole about $12,000 in merchandise and $300 in cash, and the worker confronted them.
The dispute spilled outside, where one of the men opened fire.
The worker was struck in the torso and the left arm.
He was taken to the hospital with non-life-threatening injuries.
The three men fled, possibly in a black sedan.
No arrests have been made.
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Anyone with information about the case is urged to contact police.
Call the NYPD's Crime Stoppers Hotline at 1-800-577-TIPS (8477) or for Spanish, 1-888-57-PISTA (74782). You can also submit tips by visiting the CrimeStoppers website at crimestoppers.nypdonline.org or by messaging on Twitter @NYPDTips.
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