in cricket if the wicket keeper knocks the bails off the stumps in the...

If the batsman running to the wicket has made it over the crease before the bails are off, then he is still in the game. If not, then he is out.
The batsman just has to have any part of himself or his bat over the crease, and touching the ground. And the bat must still be in his hand.
 
If all the three stumps are on the ground, he has to pick one with balls in his hand and if the batsmen is out of crease, he would be declared out. If on the other hand, if one or two stumps in place, but no bails, he has to pick one of them with ball in hand(As Bangladeshi keeper did to get Prior out).
 
Your question is a bit hard to understand. If I am understanding it right you are making out that the keeper has broken the stumps without the ball in his gloves. After they have been broken the ball comes in to his gloves for a run out. If that happened the only way the batsman would be out run out is if the keeper pulled the stumps out of the ground with the ball in hand and the batsman was still out of the crease.
 
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