If you do not wish to change the utility, you might consider using a script to achieve the transformation. The <APPLY> task would specify a shell script as the executable, and the script would invoke the target utility. The script itself would be self contained within the build.xml. Something similar to the following should work.
<project default="go"> <target name="utility.sh"> <echo file="utility.sh" append="false">#!/bin/bash utility $1 blah$1 $2 </echo> </target> <target name="go" depends="utility.sh"> <apply executable="sh"> <!-- sh command switches as args go here --> <arg value="./utility.sh"/> <srcfile/> <mapper type="glob" from="*.in" to="*.in.done"/> </apply> </target> </project>