Assuming that the virtual machine is running, to stop the machine:
– Make a list of the running virtual machines and note the ID of the one concerned.
xl list
Lets suppose the ID of the virtual machine concerned is 15

– Shutdown the machine.
xl shutdown 15
– Make a few xm list commands till the status shows as —s—.

– Then destroy the instance with
xl destroy 15
The virtual machine should have disappeared from the list (xm list)

– If so than restart the virtual machine with.
xl create /path/to/vm_config_file.cfg

– OR restart the virtual machine with DOMU console.
xl create /path/to/vm_config_file.cfg -c

– Verify the running:
xl list
Status should be
-b---- or r------

UPDATE: In Debian Wheezy it is recommended to change the XenToolStack from XM to XL because XM will soon be obsolete. The command would then be xl instead of xm. The command options are just about the same except that ‘xl’ has many more options.
To do the migration see the article:
http://tipstricks.itmatrix.eu/?s=xl&x=0&y=0