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Unfortunately there is currently no way of comparing multiple databases in a single call of sqlcompare.exe. You can however specify the object type using the "/include" option when calling sqlcompare.exe through command line. If you are unfamiliar with the include option you can familiarize yourself by calling "sqlcompare /?" from the command line.
More information available at this link.
http://www.red-gate.com/supportcenter/Content/SQL_Compare/help/10.0/SC_CL_Getting_Started -
Another approach is to create a filter in SQL Compare and to reference it in the command line using /filter
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In my continuous integration app I want to call SQLCompare.exe and tell it to only compare a list of object in each database. Is there a way of doing this? If so, please provide an example if possible.