...
<phase>generate-resources</phase>
...
<copy overwrite="true"
      file="${project.basedir}/src/main/webapp/js/my_file.js"
      toFile="${project.basedir}/target/${project.build.finalName}/js/my_file.js">
    <filterset begintoken="@@@" endtoken="@@@">
        <filter token="TOKEN_NAME" value="NEW_VALUE"/>
    </filterset>
</copy>
...

<properties>
    <my_prop>value</my_prop>
</properties>
...
<resource>
    <directory>${project.basedir}/src/main/webapp/js</directory>
    <targetPath>${project.basedir}/target/${project.build.finalName}/js</targetPath>
    <includes><include>container.jsp</include></includes>
    <filtering>true</filtering>
</resource>