If you start tomcat from startup.bat, you need to add a system variable :JAVA_OPTS as name and the parameters that you wants (in your case :
-agentpath:C:\calltracer\jvmti\calltracer5.dll=traceFile-C:\calltracer\call.trace,filterFile-C:\calltracer\filters.txt,outputType-xml,usage-uncontrolled -Djava.library.path=C:\calltracer\jvmti -Dcalltracerlib=calltracer5