FYI: I had the same issue with Visual Studio 2015. After many of hours trying, I can now do msbuild myproject.csproj /p:DeployOnBuild=true /p:PublishProfile=myprofile
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I had to edit my .csproj file to get it working. It contained a line like this:
<Import Project="$(MSBuildExtensionsPath32)\Microsoft\VisualStudio\v10.0\WebApplications\Microsoft.WebApplication.targets"
Condition="false" />
I changed this line as follows:
<Import Project="$(MSBuildExtensionsPath32)\Microsoft\VisualStudio\v14.0\WebApplications\Microsoft.WebApplication.targets" />
(I changed 10.0 to 14.0, not sure whether this was necessary. But I definitely had to remove the condition part.)