maybe see:
http://ant.apache.org/faq.html#batch-shell-execute
http://ant.apache.org/faq.html#shell-redirect-2
to run awk from a task

an example build file

<project name="noblanks" default="noblanklines" basedir=".">
   <description>
       demonstrate using awk from ant
   </description>
 <!-- set global properties for this build -->
 <property name="javadir" location="C:\Sun\AppServer\jdk\bin"/>
 <target name="noblanklines">
   <exec dir="${javadir}" executable="java.exe" os="Windows XP"
output="testout.txt">
     <arg value="-jar"/>
     <arg value="c:\libraries\java\jawk\jawk.0_11.jar"/>
     <arg value="/./"/>
     <arg value="c:\test\test.txt"/>
   </exec>
 </target>
</project>

for test.txt equals
This is line 1.

This is line 2.

This is line 3.

This is line 4.

produces testout.txt equals
This is line 1.
This is line 2.
This is line 3.
This is line 4.
on my machine