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Hi BobTheBuilder,
The GUI functionality isn't part of the comparison and so this isn't in the command line version of the tool. The best way to achieve this would be to use SQLCMD inside your CMD script to create the database before calling a comparison.
Please do let me know if you need any further assistance in the future.
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sqlcompare.exe /server1:serverA /username1: /password1: /database1:database /server2:serverB /username2: /password2: /database2:database /include:identical /sync