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Hi @Ballinhuge,
if you go to the project properties, you can specify only the where filter for comparing data (and also the columns to be considered). The comparison process should be made between objects, not queries. If you mean different Where conditions, you can (as described before) but otherwise, I guess you should compare the queries manually.
About the automation, the tool creates a deploy script and preview the differences for you, but when you compare objects.
Please, let me know if I got it correctly.
ciao,
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SQL Data Compare command line documentation:
https://documentation.red-gate.com/display/SDC12/Using+the+command+line -
If you need more flexibility than is provided by a WHERE clause, you could always create views containing your queries and compare those.
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Thank you