You can use the VCFileConfiguration class defined in the
Microsoft.VisualStudio.VCProjectEngine namespace, to set up a custom build
rule similar to how I did it with the macro below. This will probably get
you moving in the right direction.

   Sub SetCustomBuild()

       Dim pane As OutputWindowPane = GetMiscDumpPane()

       Dim prj As VCProject = DTE.Solution.Projects.Item(1).Object
       Dim files As IVCCollection = prj.Files
       Dim file As VCFile = files.Item("somesourcefile.cpp")

       Dim vcConfig As VCConfiguration = prj.Configurations("Debug|Win32")
       Dim fileConfig As VCFileConfiguration =
file.FileConfigurations("Debug|Win32")
       fileConfig.Tool = vcConfig.Tools("VCCustomBuildTool")
       fileConfig.Tool.CommandLine = "mytool.exe $(InputPath)"
       fileConfig.Tool.Description = "My custom tool"
       fileConfig.Tool.AdditionalDependencies = "None"
       fileConfig.Tool.Outputs = "$(OUTPUTDIR)\$(InputName).yes"

   End Sub

Sincerely,
Ed Dore [MSFT]

This post is 'AS IS' with no warranties, and confers no rights.