From 3e54e131e0c6484e7d12f428dbd0af9409c9dbc0 Mon Sep 17 00:00:00 2001
From: hanna <hanna@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 21 Jan 2010 19:22:56 +0000
Subject: [PATCH] Cleanup and formatting overhaul.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2652 348d0f76-0448-11de-a6fe-93d51630548a
---
 packages/Aligner.xml                      |  8 +--
 packages/AnalyzeCovariates.xml            | 22 +++----
 packages/CreatePackager.xsl               | 38 ++++++------
 packages/FindContaminatingReadGroups.xml  | 12 ++--
 packages/FixBAMSortOrder.xml              | 13 ++--
 packages/GATK-GSA-Pipeline.xml            | 26 ++++----
 packages/GATK-Picard.xml                  | 74 +++++++++++------------
 packages/GATKResources.xml                | 31 +++++-----
 packages/GenomeAnalysisTK.xml             | 68 ++++++++++-----------
 packages/LocalRealignmentAroundIndels.xml | 26 ++++----
 packages/PicardPrivate.xml                | 52 ++++++++--------
 packages/QualityScoresRecalibration.xml   | 24 ++++----
 packages/UnifiedGenotyper.xml             | 12 ++--
 packages/VCFValidator.xml                 | 12 ++--
 packages/VariantAnnotator.xml             | 26 ++++----
 packages/VariantEval.xml                  | 12 ++--
 packages/VariantFiltration.xml            | 12 ++--
 17 files changed, 218 insertions(+), 250 deletions(-)

diff --git a/packages/Aligner.xml b/packages/Aligner.xml
index cdb154648..031dfacfd 100644
--- a/packages/Aligner.xml
+++ b/packages/Aligner.xml
@@ -1,11 +1,9 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<package>
-  <name>Aligner</name>
-  <executable>
-    <name>Aligner</name>
+<package name="Aligner">
+  <executable name="Aligner">
     <dependencies>
       <!-- BWA/C aligner implementation -->
-      <class>org.broadinstitute.sting.alignment.bwa.c.BWACAligner</class>
+      <class name="org.broadinstitute.sting.alignment.bwa.c.BWACAligner" />
     </dependencies>
   </executable>
 </package>
diff --git a/packages/AnalyzeCovariates.xml b/packages/AnalyzeCovariates.xml
index db62081f9..1ad7be3d7 100644
--- a/packages/AnalyzeCovariates.xml
+++ b/packages/AnalyzeCovariates.xml
@@ -1,18 +1,16 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<package>
-  <name>AnalyzeCovariates</name>
-  <executable>
-    <name>AnalyzeCovariates</name>
-    <main-class>org.broadinstitute.sting.analyzecovariates.AnalyzeCovariates</main-class>
-    <properties>StingText.properties</properties>
+<package name="AnalyzeCovariates">
+  <executable name="AnalyzeCovariates">
+    <main-class name="org.broadinstitute.sting.analyzecovariates.AnalyzeCovariates" />
+    <resource-bundle file="StingText.properties" />
     <dependencies>
       <!-- Recalibration analysis script -->
-      <class>org.broadinstitute.sting.analyzecovariates.AnalyzeCovariates</class>
-      <class>org.broadinstitute.sting.gatk.walkers.recalibration.DinucCovariate</class>
-      <class>org.broadinstitute.sting.gatk.walkers.recalibration.QualityScoreCovariate</class>
-      <class>org.broadinstitute.sting.gatk.walkers.recalibration.CycleCovariate</class>
-      <class>org.broadinstitute.sting.gatk.walkers.recalibration.ReadGroupCovariate</class>
-      <class>org.broadinstitute.sting.gatk.walkers.recalibration.TileCovariate</class>
+      <class name="org.broadinstitute.sting.analyzecovariates.AnalyzeCovariates" />
+      <class name=">org.broadinstitute.sting.gatk.walkers.recalibration.DinucCovariate" />
+      <class name=">org.broadinstitute.sting.gatk.walkers.recalibration.QualityScoreCovariate" />
+      <class name=">org.broadinstitute.sting.gatk.walkers.recalibration.CycleCovariate" />
+      <class name=">org.broadinstitute.sting.gatk.walkers.recalibration.ReadGroupCovariate" />
+      <class name=">org.broadinstitute.sting.gatk.walkers.recalibration.TileCovariate" />
     </dependencies>
   </executable>
 </package>
diff --git a/packages/CreatePackager.xsl b/packages/CreatePackager.xsl
index 15274c7f3..38f3f9004 100644
--- a/packages/CreatePackager.xsl
+++ b/packages/CreatePackager.xsl
@@ -12,7 +12,7 @@
 <xsl:template match="package">
   <xsl:output method="xml" indent="yes"/>
 
-  <xsl:variable name="project.name" select="name" />
+  <xsl:variable name="project.name" select="@name" />
 
   <project name="{$project.name}" default="package">
     <property name="sting.dir" value="{$ant.basedir}" />
@@ -21,12 +21,12 @@
     <target name="package">
       <!-- Verify that all classes specified are present -->
       <xsl:for-each select="//class">
-	<available property="is.{current()}.present" classpath="{$classpath}" classname="{current()}"/>
-	<fail message="Class {current()} not found" unless="is.{current()}.present" />
+	<available property="is.{@name}.present" classpath="{$classpath}" classname="{@name}"/>
+	<fail message="Class {@name} not found" unless="is.{@name}.present" />
       </xsl:for-each>
       <xsl:for-each select="//resource-bundle">
-	<available property="is.{current()}.present" file="{$staging.dir}/{current()}"/>
-	<fail message="Resource bundle {current()} not found" unless="is.{current()}.present" />
+	<available property="is.{@file}.present" file="{$staging.dir}/{@file}"/>
+	<fail message="Resource bundle {@file} not found" unless="is.{@file}.present" />
       </xsl:for-each>
 
       <!-- Create an output directory for the package -->
@@ -37,13 +37,13 @@
 
       <!-- Add in other modules -->
       <xsl:for-each select="modules/module">
-	<xsl:apply-templates select="document(current())/package/executable" />
+	<xsl:apply-templates select="document(@file)/package/executable" />
       </xsl:for-each>
 
       <!-- Include various script files -->
       <xsl:for-each select="scripts/file">
         <xsl:call-template name="symlink">
-          <xsl:with-param name="file.name" select="." />
+          <xsl:with-param name="file.name" select="@name" />
           <xsl:with-param name="target.dir" select="$package.dir" />
         </xsl:call-template>
       </xsl:for-each>
@@ -52,7 +52,7 @@
       <xsl:for-each select="resources/file">
         <mkdir dir="{$resources.dir}"/>
         <xsl:call-template name="symlink">
-          <xsl:with-param name="file.name" select="." />
+          <xsl:with-param name="file.name" select="@name" />
           <xsl:with-param name="target.dir" select="$resources.dir" />
         </xsl:call-template>
       </xsl:for-each>
@@ -62,14 +62,14 @@
 	<xsl:when test="version">
 	  <property file="{$staging.dir}/{version/@file}" />
 	  <xsl:variable name="version.property" select="concat('${',version/@property,'}')" />
-	  <property name="package.filename" value="{name}-{$version.property}.tar.bz2" />
+	  <property name="package.filename" value="{@name}-{$version.property}.tar.bz2" />
 	</xsl:when>
 	<xsl:otherwise>
-	  <property name="package.filename" value="{name}.tar.bz2" />
+	  <property name="package.filename" value="{@name}.tar.bz2" />
 	</xsl:otherwise>
       </xsl:choose>
       <xsl:variable name="package.filename" select="'${package.filename}'" />
-      <tar destfile="{$dist.dir}/{$package.filename}" basedir="{$package.dir}" compression="bzip2" />
+      <tar destfile="{$dist.dir}/packages/{$package.filename}" basedir="{$package.dir}" compression="bzip2" />
     </target>
   </project>
 </xsl:template>
@@ -98,19 +98,19 @@
 <!-- Transform an executable tag into an ant 'jar' task with nested fileset -->
 <xsl:template match="executable">
   <!-- Create a jar file containing the specified classes / packages and all their dependencies -->
-  <jar jarfile="{$package.dir}/{name}.jar">
+  <jar jarfile="{$package.dir}/{@name}.jar">
     <classfileset dir="{$staging.dir}">
-      <root classname="{main-class}"/>
+      <root classname="{main-class/@name}"/>
     </classfileset>
     <xsl:for-each select="resource-bundle">
-      <fileset file="{$staging.dir}/{current()}" />
+      <fileset file="{$staging.dir}/{@file}" />
     </xsl:for-each>
     <xsl:for-each select="modules/module">
-      <xsl:apply-templates select="document(current())/package/executable/dependencies" />
+      <xsl:apply-templates select="document(@file)/package/executable/dependencies" />
     </xsl:for-each>
     <xsl:apply-templates select="dependencies" />
     <manifest>
-      <attribute name="Main-Class" value="{main-class}"/>
+      <attribute name="Main-Class" value="{main-class/@name}"/>
     </manifest>
   </jar>
 </xsl:template>
@@ -119,14 +119,14 @@
 <xsl:template match="dependencies">
   <classfileset dir="{$staging.dir}">
     <xsl:for-each select="package">
-      <rootfileset dir="{$staging.dir}" includes="{concat(translate(current(),'.','/'),'/','*.class')}" />
+      <rootfileset dir="{$staging.dir}" includes="{concat(translate(@name,'.','/'),'/','*.class')}" />
     </xsl:for-each>
     <xsl:for-each select="class">
-      <root classname="{current()}" />
+      <root classname="{@name}" />
     </xsl:for-each>
   </classfileset>
   <xsl:for-each select="file">
-    <fileset file="{$staging.dir}/{current()}" />
+    <fileset file="{$staging.dir}/{@name}" />
   </xsl:for-each>
 </xsl:template>
 
diff --git a/packages/FindContaminatingReadGroups.xml b/packages/FindContaminatingReadGroups.xml
index e2c6cb9d9..880f64a81 100644
--- a/packages/FindContaminatingReadGroups.xml
+++ b/packages/FindContaminatingReadGroups.xml
@@ -1,12 +1,10 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<package>
-  <name>FindContaminatingReadGroups</name>
-  <executable>
-    <name>FindContaminatingReadGroups</name>
-    <main-class>org.broadinstitute.sting.gatk.CommandLineGATK</main-class>
-    <properties>StingText.properties</properties>
+<package name="FindContaminatingReadGroups">
+  <executable name="FindContaminatingReadGroups">
+    <main-class name="org.broadinstitute.sting.gatk.CommandLineGATK" />
+    <resource-bundle file="StingText.properties" />
     <dependencies>
-      <class>org.broadinstitute.sting.playground.gatk.walkers.contamination.FindContaminatingReadGroupsWalker</class>
+      <class name="org.broadinstitute.sting.playground.gatk.walkers.contamination.FindContaminatingReadGroupsWalker" />
     </dependencies>
   </executable>
 </package>
diff --git a/packages/FixBAMSortOrder.xml b/packages/FixBAMSortOrder.xml
index 1c9491f32..6a110e637 100644
--- a/packages/FixBAMSortOrder.xml
+++ b/packages/FixBAMSortOrder.xml
@@ -1,14 +1,11 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<package>
-  <name>FixBAMSortOrder</name>
-  <executable>
-    <name>GenomeAnalysisTK</name>
-    <main-class>org.broadinstitute.sting.gatk.CommandLineGATK</main-class>
+<package name="FixBAMSortOrder">
+  <executable name="FixBAMSortOrder">
+    <main-class name="org.broadinstitute.sting.gatk.CommandLineGATK" />
+    <resource-bundle file="StingText.properties" />
     <dependencies>
-      <!-- Text extracted from the javadocs -->
-      <properties>StingText.properties</properties>
       <!-- The walker -->
-      <class>org.broadinstitute.sting.gatk.walkers.FixBAMSortOrderTag</class>
+      <class name="org.broadinstitute.sting.gatk.walkers.FixBAMSortOrderTag" />
     </dependencies>
   </executable>
 </package>
diff --git a/packages/GATK-GSA-Pipeline.xml b/packages/GATK-GSA-Pipeline.xml
index 226077e22..0d64f4224 100644
--- a/packages/GATK-GSA-Pipeline.xml
+++ b/packages/GATK-GSA-Pipeline.xml
@@ -1,25 +1,23 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!-- NOTE: Uses playground.
      ant clean playground package -Dexecutable=GATK-GSA-Pipeline -->
-<package>
-  <name>GATK-GSA-Pipeline</name>
+<package name="GATK-GSA-Pipeline">
   <version file="StingText.properties" property="org.broadinstitute.sting.gatk.version" />
-  <executable>
-    <name>GATK-GSA-Pipeline</name>
-    <main-class>org.broadinstitute.sting.gatk.CommandLineGATK</main-class>
-    <resource-bundle>StingText.properties</resource-bundle>
+  <executable name="GATK-GSA-Pipeline">
+    <main-class name="org.broadinstitute.sting.gatk.CommandLineGATK" />
+    <resource-bundle file="StingText.properties" />
     <modules>
-      <module>QualityScoresRecalibration.xml</module>
-      <module>LocalRealignmentAroundIndels.xml</module>
-      <module>UnifiedGenotyper.xml</module>
-      <module>VariantFiltration.xml</module>
-      <module>VariantAnnotator.xml</module>
-      <module>VariantEval.xml</module>
-      <module>FindContaminatingReadGroups.xml</module>
+      <module name="QualityScoresRecalibration.xml" />
+      <module name="LocalRealignmentAroundIndels.xml" />
+      <module name="UnifiedGenotyper.xml" />
+      <module name="VariantFiltration.xml" />
+      <module name="VariantAnnotator.xml" />
+      <module name="VariantEval.xml" />
+      <module name="FindContaminatingReadGroups.xml" />
     </modules>
     <dependencies>
       <!-- Filters -->
-      <package>org.broadinstitute.sting.gatk.filters</package>
+      <package name="org.broadinstitute.sting.gatk.filters" />
     </dependencies>
   </executable>
 </package>
diff --git a/packages/GATK-Picard.xml b/packages/GATK-Picard.xml
index f43069d9b..ae04f9177 100644
--- a/packages/GATK-Picard.xml
+++ b/packages/GATK-Picard.xml
@@ -2,55 +2,53 @@
         <!-- In order to update this file, copy GenomeAnalysisTK.xml, change the name of the
         package and executable to GATK-Picard, and add TileCovariate to the list of dependencies.
         Remove the AnalyzeCovariates executable. -->
-<package>
-  <name>GATK-Picard</name>
+<package name="GATK-Picard">
   <version file="StingText.properties" property="org.broadinstitute.sting.gatk.version" />
-  <executable>
-    <name>GATK-Picard</name>
-    <main-class>org.broadinstitute.sting.gatk.CommandLineGATK</main-class>
-    <resource-bundle>StingText.properties</resource-bundle>
+  <executable name="GATK-Picard">
+    <main-class name="org.broadinstitute.sting.gatk.CommandLineGATK" />
+    <resource-bundle file="StingText.properties" />
     <modules>
-      <module>QualityScoresRecalibration.xml</module>
-      <module>LocalRealignmentAroundIndels.xml</module>
-      <module>UnifiedGenotyper.xml</module>
-      <module>VariantFiltration.xml</module>
-      <module>VariantAnnotator.xml</module>
+      <module name="QualityScoresRecalibration.xml" />
+      <module name="LocalRealignmentAroundIndels.xml" />
+      <module name="UnifiedGenotyper.xml" />
+      <module name="VariantFiltration.xml" />
+      <module name="VariantAnnotator.xml" />
     </modules>
     <dependencies>
       <!-- Filters -->
-      <package>org.broadinstitute.sting.gatk.filters</package>
-      <class>org.broadinstitute.sting.gatk.walkers.coverage.DepthOfCoverageWalker</class>
-      <class>org.broadinstitute.sting.gatk.walkers.PileupWalker</class>
-      <class>org.broadinstitute.sting.gatk.walkers.PrintReadsWalker</class>
-      <class>org.broadinstitute.sting.gatk.walkers.qc.CountLociWalker</class>
-      <class>org.broadinstitute.sting.gatk.walkers.qc.CountReadsWalker</class>
-      <class>org.broadinstitute.sting.gatk.walkers.qc.ValidatingPileupWalker</class>
+      <package name="org.broadinstitute.sting.gatk.filters" />
+      <class name="org.broadinstitute.sting.gatk.walkers.coverage.DepthOfCoverageWalker" />
+      <class name="org.broadinstitute.sting.gatk.walkers.PileupWalker" />
+      <class name="org.broadinstitute.sting.gatk.walkers.PrintReadsWalker" />
+      <class name="org.broadinstitute.sting.gatk.walkers.qc.CountLociWalker" />
+      <class name="org.broadinstitute.sting.gatk.walkers.qc.CountReadsWalker" />
+      <class name="org.broadinstitute.sting.gatk.walkers.qc.ValidatingPileupWalker" />
       <!-- Recalibration Covariates -->
-      <class>org.broadinstitute.sting.gatk.walkers.recalibration.PositionCovariate</class>
-      <class>org.broadinstitute.sting.gatk.walkers.recalibration.MinimumNQSCovariate</class>
-      <class>org.broadinstitute.sting.gatk.walkers.recalibration.MappingQualityCovariate</class>
-      <class>org.broadinstitute.sting.gatk.walkers.recalibration.PrimerRoundCovariate</class>
-      <class>org.broadinstitute.sting.gatk.walkers.recalibration.HomopolymerCovariate</class>
+      <class name="org.broadinstitute.sting.gatk.walkers.recalibration.PositionCovariate" />
+      <class name="org.broadinstitute.sting.gatk.walkers.recalibration.MinimumNQSCovariate" />
+      <class name="org.broadinstitute.sting.gatk.walkers.recalibration.MappingQualityCovariate" />
+      <class name="org.broadinstitute.sting.gatk.walkers.recalibration.PrimerRoundCovariate" />
+      <class name="org.broadinstitute.sting.gatk.walkers.recalibration.HomopolymerCovariate" />
     </dependencies>
   </executable>
   <resources>
     <!-- GATK sample code and build scripts -->
-    <file>java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java</file>
-    <file>java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java</file>
-    <file>java/src/org/broadinstitute/sting/gatk/walkers/PrintReadsWalker.java</file>
-    <file>java/src/org/broadinstitute/sting/gatk/walkers/qc/CountLociWalker.java</file>
-    <file>java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReadsWalker.java</file>
-    <file>java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileupWalker.java</file>
-    <file>java/src/org/broadinstitute/sting/gatk/examples/HelloWalker.java</file>
-    <file>java/src/org/broadinstitute/sting/gatk/examples/build.xml</file>
+    <file name="java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java" />
+    <file name="java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java" />
+    <file name="java/src/org/broadinstitute/sting/gatk/walkers/PrintReadsWalker.java" />
+    <file name="java/src/org/broadinstitute/sting/gatk/walkers/qc/CountLociWalker.java" />
+    <file name="java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReadsWalker.java" />
+    <file name="java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileupWalker.java" />
+    <file name="java/src/org/broadinstitute/sting/gatk/examples/HelloWalker.java" />
+    <file name="java/src/org/broadinstitute/sting/gatk/examples/build.xml" />
     <!-- Sample reads and reference files -->
-    <file>testdata/exampleBAM.bam</file>
-    <file>testdata/exampleBAM.bam.bai</file>
-    <file>testdata/exampleFASTA.fasta</file>
-    <file>testdata/exampleFASTA.fasta.fai</file>
-    <file>testdata/exampleFASTA.dict</file>
+    <file name="testdata/exampleBAM.bam" />
+    <file name="testdata/exampleBAM.bam.bai" />
+    <file name="testdata/exampleFASTA.fasta" />
+    <file name="testdata/exampleFASTA.fasta.fai" />
+    <file name="testdata/exampleFASTA.dict" />
     <!-- Supplemental scripts for graph generation, etc. -->
-    <file>R/plot_residualError_OtherCovariate.R</file>
-    <file>R/plot_residualError_QualityScoreCovariate.R</file>
+    <file name="R/plot_residualError_OtherCovariate.R" />
+    <file name="R/plot_residualError_QualityScoreCovariate.R" />
   </resources>
 </package>
diff --git a/packages/GATKResources.xml b/packages/GATKResources.xml
index 0a87154d4..50e3ca7f2 100755
--- a/packages/GATKResources.xml
+++ b/packages/GATKResources.xml
@@ -1,20 +1,19 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<package>
-  <name>GATKResources</name>
+<package name="GATKResources">
   <resources>
-    <file>/humgen/gsa-scr1/GATK_Data/dbsnp_129_b36.rod</file>
-    <file>/humgen/gsa-scr1/GATK_Data/dbsnp_130_b36.rod</file>
-    <file>/broad/1KG/reference/human_b36_both.fasta</file>
-    <file>/broad/1KG/reference/human_b36_both.dict</file>
-    <file>/broad/1KG/reference/human_b36_both.fasta.fai</file>
-    <file>/humgen/gsa-scr1/GATK_Data/dbsnp_129_hg18.rod</file>
-    <file>/humgen/gsa-scr1/GATK_Data/dbsnp_130_hg18.rod</file>
-    <file>/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta</file>
-    <file>/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.dict</file>
-    <file>/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta.fai</file>
-    <file>/humgen/gsa-scr1/GATK_Data/dbsnp_130_b37.rod</file>
-    <file>/broad/1KG/reference/human_g1k_v37.fasta</file>
-    <file>/broad/1KG/reference/human_g1k_v37.dict</file>
-    <file>/broad/1KG/reference/human_g1k_v37.fasta.fai</file>
+    <file name="/humgen/gsa-scr1/GATK_Data/dbsnp_129_b36.rod" />
+    <file name="/humgen/gsa-scr1/GATK_Data/dbsnp_130_b36.rod" />
+    <file name="/broad/1KG/reference/human_b36_both.fasta" />
+    <file name="/broad/1KG/reference/human_b36_both.dict" />
+    <file name="/broad/1KG/reference/human_b36_both.fasta.fai" />
+    <file name="/humgen/gsa-scr1/GATK_Data/dbsnp_129_hg18.rod" />
+    <file name="/humgen/gsa-scr1/GATK_Data/dbsnp_130_hg18.rod" />
+    <file name="/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta" />
+    <file name="/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.dict" />
+    <file name="/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta.fai" />
+    <file name="/humgen/gsa-scr1/GATK_Data/dbsnp_130_b37.rod" />
+    <file name="/broad/1KG/reference/human_g1k_v37.fasta" />
+    <file name="/broad/1KG/reference/human_g1k_v37.dict" />
+    <file name="/broad/1KG/reference/human_g1k_v37.fasta.fai" />
    </resources>
 </package>
diff --git a/packages/GenomeAnalysisTK.xml b/packages/GenomeAnalysisTK.xml
index 8927106b1..4ae5d6819 100644
--- a/packages/GenomeAnalysisTK.xml
+++ b/packages/GenomeAnalysisTK.xml
@@ -1,52 +1,50 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<package>
-  <name>GenomeAnalysisTK</name>
+<package name="GenomeAnalysisTK">
   <version file="StingText.properties" property="org.broadinstitute.sting.gatk.version" />
-  <executable>
-    <name>GenomeAnalysisTK</name>
-    <main-class>org.broadinstitute.sting.gatk.CommandLineGATK</main-class>
-    <resource-bundle>StingText.properties</resource-bundle>
+  <executable name="GenomeAnalysisTK">
+    <main-class name="org.broadinstitute.sting.gatk.CommandLineGATK" />
+    <resource-bundle file="StingText.properties" />
     <modules>
-      <module>QualityScoresRecalibration.xml</module>
-      <module>LocalRealignmentAroundIndels.xml</module>
-      <module>UnifiedGenotyper.xml</module>
-      <module>VariantFiltration.xml</module>
-      <module>VariantAnnotator.xml</module>
-      <module>VCFValidator.xml</module>
+      <module file="QualityScoresRecalibration.xml" />
+      <module file="LocalRealignmentAroundIndels.xml" />
+      <module file="UnifiedGenotyper.xml" />
+      <module file="VariantFiltration.xml" />
+      <module file="VariantAnnotator.xml" />
+      <module file="VCFValidator.xml" />
     </modules>
     <dependencies>
       <!-- Filters -->
-      <package>org.broadinstitute.sting.gatk.filters</package>
+      <package name="org.broadinstitute.sting.gatk.filters" />
       <!-- Basic qc walkers -->
-      <class>org.broadinstitute.sting.gatk.walkers.coverage.DepthOfCoverageWalker</class>
-      <class>org.broadinstitute.sting.gatk.walkers.PileupWalker</class>
-      <class>org.broadinstitute.sting.gatk.walkers.PrintReadsWalker</class>
-      <class>org.broadinstitute.sting.gatk.walkers.qc.CountLociWalker</class>
-      <class>org.broadinstitute.sting.gatk.walkers.qc.CountReadsWalker</class>
-      <class>org.broadinstitute.sting.gatk.walkers.qc.ValidatingPileupWalker</class>
+      <class name="org.broadinstitute.sting.gatk.walkers.coverage.DepthOfCoverageWalker" />
+      <class name="org.broadinstitute.sting.gatk.walkers.PileupWalker" />
+      <class name="org.broadinstitute.sting.gatk.walkers.PrintReadsWalker" />
+      <class name="org.broadinstitute.sting.gatk.walkers.qc.CountLociWalker" />
+      <class name="org.broadinstitute.sting.gatk.walkers.qc.CountReadsWalker" />
+      <class name="org.broadinstitute.sting.gatk.walkers.qc.ValidatingPileupWalker" />
     </dependencies>
   </executable>
   <modules>
-    <module>AnalyzeCovariates.xml</module>
+    <module file="AnalyzeCovariates.xml"/>
   </modules>
   <resources>
     <!-- GATK sample code and build scripts -->
-    <file>java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java</file>
-    <file>java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java</file>
-    <file>java/src/org/broadinstitute/sting/gatk/walkers/PrintReadsWalker.java</file>
-    <file>java/src/org/broadinstitute/sting/gatk/walkers/qc/CountLociWalker.java</file>
-    <file>java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReadsWalker.java</file>
-    <file>java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileupWalker.java</file>
-    <file>java/src/org/broadinstitute/sting/gatk/examples/HelloWalker.java</file>
-    <file>java/src/org/broadinstitute/sting/gatk/examples/build.xml</file>
+    <file name="java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java" />
+    <file name="java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java" />
+    <file name="java/src/org/broadinstitute/sting/gatk/walkers/PrintReadsWalker.java" />
+    <file name="java/src/org/broadinstitute/sting/gatk/walkers/qc/CountLociWalker.java" />
+    <file name="java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReadsWalker.java" />
+    <file name="java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileupWalker.java" />
+    <file name="java/src/org/broadinstitute/sting/gatk/examples/HelloWalker.java" />
+    <file name="java/src/org/broadinstitute/sting/gatk/examples/build.xml" />
     <!-- Sample reads and reference files -->
-    <file>testdata/exampleBAM.bam</file>
-    <file>testdata/exampleBAM.bam.bai</file>
-    <file>testdata/exampleFASTA.fasta</file>
-    <file>testdata/exampleFASTA.fasta.fai</file>
-    <file>testdata/exampleFASTA.dict</file>
+    <file name="testdata/exampleBAM.bam" />
+    <file name="testdata/exampleBAM.bam.bai" />
+    <file name="testdata/exampleFASTA.fasta" />
+    <file name="testdata/exampleFASTA.fasta.fai" />
+    <file name="testdata/exampleFASTA.dict" />
     <!-- Supplemental scripts for graph generation, etc. -->
-    <file>R/plot_residualError_OtherCovariate.R</file>
-    <file>R/plot_residualError_QualityScoreCovariate.R</file>
+    <file name="R/plot_residualError_OtherCovariate.R" />
+    <file name="R/plot_residualError_QualityScoreCovariate.R" />
   </resources>
 </package>
diff --git a/packages/LocalRealignmentAroundIndels.xml b/packages/LocalRealignmentAroundIndels.xml
index 1a443a106..a3cb273a1 100644
--- a/packages/LocalRealignmentAroundIndels.xml
+++ b/packages/LocalRealignmentAroundIndels.xml
@@ -1,20 +1,18 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<package>
-  <name>LocalRealignmentAroundIndels</name>
-  <executable>
-    <name>LocalRealignmentAroundIndels</name>
-    <main-class>org.broadinstitute.sting.gatk.CommandLineGATK</main-class>
-    <properties>StingText.properties</properties>
+<package name="LocalRealignmentAroundIndels">
+  <executable name="LocalRealignmentAroundIndels">
+    <main-class name="org.broadinstitute.sting.gatk.CommandLineGATK" />
+    <resource-bundle file="StingText.properties" />
     <dependencies>
       <!-- Local realignment around indels -->
-      <class>org.broadinstitute.sting.gatk.walkers.indels.CleanedReadInjector</class>
-      <class>org.broadinstitute.sting.gatk.walkers.indels.IndelIntervalWalker</class>
-      <class>org.broadinstitute.sting.gatk.walkers.indels.IntervalCleanerWalker</class>
-      <class>org.broadinstitute.sting.gatk.walkers.indels.IntervalMergerWalker</class>
-      <class>org.broadinstitute.sting.gatk.walkers.indels.MismatchIntervalWalker</class>
-      <class>org.broadinstitute.sting.gatk.walkers.indels.SNPClusterWalker</class>
-      <class>org.broadinstitute.sting.gatk.walkers.indels.IndelGenotyperWalker</class>
-      <class>org.broadinstitute.sting.gatk.walkers.indels.IndelGenotyperV2Walker</class> 
+      <class name="org.broadinstitute.sting.gatk.walkers.indels.CleanedReadInjector" />
+      <class name="org.broadinstitute.sting.gatk.walkers.indels.IndelIntervalWalker" />
+      <class name="org.broadinstitute.sting.gatk.walkers.indels.IntervalCleanerWalker" />
+      <class name="org.broadinstitute.sting.gatk.walkers.indels.IntervalMergerWalker" />
+      <class name="org.broadinstitute.sting.gatk.walkers.indels.MismatchIntervalWalker" />
+      <class name="org.broadinstitute.sting.gatk.walkers.indels.SNPClusterWalker" />
+      <class name="org.broadinstitute.sting.gatk.walkers.indels.IndelGenotyperWalker" />
+      <class name="org.broadinstitute.sting.gatk.walkers.indels.IndelGenotyperV2Walker" /> 
     </dependencies>
   </executable>
 </package>
diff --git a/packages/PicardPrivate.xml b/packages/PicardPrivate.xml
index 6a424cc6d..06f5235c7 100644
--- a/packages/PicardPrivate.xml
+++ b/packages/PicardPrivate.xml
@@ -1,32 +1,30 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<package>
-  <name>picard-private-parts</name>
-  <executable>
-    <name>picard-private-parts</name>
+<package name="picard-private-parts">
+  <executable name="picard-private-parts">
     <dependencies>
-      <class>edu.mit.broad.picard.directed.IntervalList</class>
-      <class>edu.mit.broad.picard.genotype.DiploidGenotype</class>
-      <class>edu.mit.broad.picard.genotype.geli.GeliFileReader</class>
-      <class>edu.mit.broad.picard.genotype.geli.GeliFileWriter</class>
-      <class>edu.mit.broad.picard.genotype.geli.GenotypeLikelihoods</class>
-      <class>edu.mit.broad.picard.util.BasicTextFileParser</class>
-      <class>edu.mit.broad.picard.illumina.parser.IlluminaUtil</class>
-      <class>edu.mit.broad.picard.util.Interval</class>
-      <class>edu.mit.broad.picard.util.IntervalTree</class>
-      <class>edu.mit.broad.picard.util.OverlapDetector</class>
-      <class>edu.mit.broad.picard.util.PasteParser</class>
-      <class>edu.mit.broad.picard.variation.KnownVariantCodecV2</class>
-      <class>edu.mit.broad.picard.variation.KnownVariantCodec</class>
-      <class>edu.mit.broad.picard.variation.KnownVariantFileHeader</class>
-      <class>edu.mit.broad.picard.variation.GenerateDbSnpFile</class>
-      <class>edu.mit.broad.picard.variation.VariantType</class>
-      <class>edu.mit.broad.picard.variation.ObsoleteKnownVariantCodecV1</class>
-      <class>edu.mit.broad.picard.variation.AbstractKnownVariantCodec</class>
-      <class>edu.mit.broad.picard.variation.KnownVariantIterator</class>
-      <class>edu.mit.broad.picard.variation.KnownVariantCodecFactory</class>
-      <class>edu.mit.broad.picard.variation.KnownVariant</class>
-      <class>edu.mit.broad.picard.variation.DbSnpFileReader</class>
-      <class>edu.mit.broad.picard.variation.DbSnpFileGenerator</class>
+      <class name="edu.mit.broad.picard.directed.IntervalList" />
+      <class name="edu.mit.broad.picard.genotype.DiploidGenotype" />
+      <class name="edu.mit.broad.picard.genotype.geli.GeliFileReader" />
+      <class name="edu.mit.broad.picard.genotype.geli.GeliFileWriter" />
+      <class name="edu.mit.broad.picard.genotype.geli.GenotypeLikelihoods" />
+      <class name="edu.mit.broad.picard.util.BasicTextFileParser" />
+      <class name="edu.mit.broad.picard.illumina.parser.IlluminaUtil" />
+      <class name="edu.mit.broad.picard.util.Interval" />
+      <class name="edu.mit.broad.picard.util.IntervalTree" />
+      <class name="edu.mit.broad.picard.util.OverlapDetector" />
+      <class name="edu.mit.broad.picard.util.PasteParser" />
+      <class name="edu.mit.broad.picard.variation.KnownVariantCodecV2" />
+      <class name="edu.mit.broad.picard.variation.KnownVariantCodec" />
+      <class name="edu.mit.broad.picard.variation.KnownVariantFileHeader" />
+      <class name="edu.mit.broad.picard.variation.GenerateDbSnpFile" />
+      <class name="edu.mit.broad.picard.variation.VariantType" />
+      <class name="edu.mit.broad.picard.variation.ObsoleteKnownVariantCodecV1" />
+      <class name="edu.mit.broad.picard.variation.AbstractKnownVariantCodec" />
+      <class name="edu.mit.broad.picard.variation.KnownVariantIterator" />
+      <class name="edu.mit.broad.picard.variation.KnownVariantCodecFactory" />
+      <class name="edu.mit.broad.picard.variation.KnownVariant" />
+      <class name="edu.mit.broad.picard.variation.DbSnpFileReader" />
+      <class name="edu.mit.broad.picard.variation.DbSnpFileGenerator" />
     </dependencies>
   </executable>
 </package>
diff --git a/packages/QualityScoresRecalibration.xml b/packages/QualityScoresRecalibration.xml
index 477ced3d0..3b43158f2 100644
--- a/packages/QualityScoresRecalibration.xml
+++ b/packages/QualityScoresRecalibration.xml
@@ -1,20 +1,18 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<package>
-  <name>QualityScoresRecalibration</name>
-  <executable>
-    <name>QualityScoresRecalibration</name>
-    <main-class>org.broadinstitute.sting.gatk.CommandLineGATK</main-class>
-    <properties>StingText.properties</properties>
+<package name="QualityScoresRecalibration">
+  <executable name="QualityScoresRecalibration">
+    <main-class name="org.broadinstitute.sting.gatk.CommandLineGATK" />
+    <resource-bundle file="StingText.properties" />
     <dependencies>
       <!-- Quality scores recalibration -->
-      <class>org.broadinstitute.sting.gatk.walkers.recalibration.CovariateCounterWalker</class>
-      <class>org.broadinstitute.sting.gatk.walkers.recalibration.TableRecalibrationWalker</class>
+      <class file="org.broadinstitute.sting.gatk.walkers.recalibration.CovariateCounterWalker" />
+      <class file=">org.broadinstitute.sting.gatk.walkers.recalibration.TableRecalibrationWalker" />
       <!-- Recalibration Covariates -->
-      <class>org.broadinstitute.sting.gatk.walkers.recalibration.DinucCovariate</class>
-      <class>org.broadinstitute.sting.gatk.walkers.recalibration.QualityScoreCovariate</class>
-      <class>org.broadinstitute.sting.gatk.walkers.recalibration.CycleCovariate</class>
-      <class>org.broadinstitute.sting.gatk.walkers.recalibration.ReadGroupCovariate</class>
-      <class>org.broadinstitute.sting.gatk.walkers.recalibration.TileCovariate</class>
+      <class file=">org.broadinstitute.sting.gatk.walkers.recalibration.DinucCovariate" />
+      <class file=">org.broadinstitute.sting.gatk.walkers.recalibration.QualityScoreCovariate" />
+      <class file=">org.broadinstitute.sting.gatk.walkers.recalibration.CycleCovariate" />
+      <class file=">org.broadinstitute.sting.gatk.walkers.recalibration.ReadGroupCovariate" />
+      <class file=">org.broadinstitute.sting.gatk.walkers.recalibration.TileCovariate" />
     </dependencies>
   </executable>
 </package>
diff --git a/packages/UnifiedGenotyper.xml b/packages/UnifiedGenotyper.xml
index 46fb26332..67a17640c 100644
--- a/packages/UnifiedGenotyper.xml
+++ b/packages/UnifiedGenotyper.xml
@@ -1,13 +1,11 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<package>
-  <name>UnifiedGenotyper</name>
-  <executable>
-    <name>UnifiedGenotyper</name>
-    <main-class>org.broadinstitute.sting.gatk.CommandLineGATK</main-class>
-    <properties>StingText.properties</properties>
+<package name="UnifiedGenotyper">
+  <executable name="UnifiedGenotyper">
+    <main-class name="org.broadinstitute.sting.gatk.CommandLineGATK" />
+    <resource-bundle file="StingText.properties" />
     <dependencies>
       <!-- Unified genotyper -->
-      <class>org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyper</class>
+      <class name="org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyper" />
     </dependencies>
   </executable>
 </package>
diff --git a/packages/VCFValidator.xml b/packages/VCFValidator.xml
index 891a1d698..f66a6cfeb 100644
--- a/packages/VCFValidator.xml
+++ b/packages/VCFValidator.xml
@@ -1,13 +1,11 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<package>
-  <name>VCFValidator</name>
-  <executable>
-    <name>VCFValidator</name>
-    <main-class>org.broadinstitute.sting.gatk.CommandLineGATK</main-class>
-    <properties>StingText.properties</properties>
+<package name="VCFValidator">
+  <executable name="VCFValidator">
+    <main-class name="org.broadinstitute.sting.gatk.CommandLineGATK" />
+    <resource-bundle file="StingText.properties" />
     <dependencies>
       <!-- VCF validator -->
-      <class>org.broadinstitute.sting.gatk.walkers.qc.VCFValidator</class>
+      <class name="org.broadinstitute.sting.gatk.walkers.qc.VCFValidator" />
     </dependencies>
   </executable>
 </package>
diff --git a/packages/VariantAnnotator.xml b/packages/VariantAnnotator.xml
index 2fa51cce0..984d5b399 100644
--- a/packages/VariantAnnotator.xml
+++ b/packages/VariantAnnotator.xml
@@ -1,21 +1,19 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<package>
-  <name>VariantAnnotator</name>
-  <executable>
-    <name>VariantAnnotator</name>
-    <main-class>org.broadinstitute.sting.gatk.CommandLineGATK</main-class>
-    <properties>StingText.properties</properties>
+<package name="VariantAnnotator">
+  <executable name="VariantAnnotator">
+    <main-class name="org.broadinstitute.sting.gatk.CommandLineGATK" />
+    <resource-bundle file="StingText.properties" />
     <dependencies>
       <!-- Variant annotator -->
-      <class>org.broadinstitute.sting.gatk.walkers.annotator.VariantAnnotator</class>
+      <class name="org.broadinstitute.sting.gatk.walkers.annotator.VariantAnnotator" />
       <!-- And the annotations -->
-      <class>org.broadinstitute.sting.gatk.walkers.annotator.AlleleBalance</class>
-      <class>org.broadinstitute.sting.gatk.walkers.annotator.DepthOfCoverage</class>
-      <class>org.broadinstitute.sting.gatk.walkers.annotator.HomopolymerRun</class>
-      <class>org.broadinstitute.sting.gatk.walkers.annotator.MappingQualityZero</class>
-      <class>org.broadinstitute.sting.gatk.walkers.annotator.QualByDepth</class>
-      <class>org.broadinstitute.sting.gatk.walkers.annotator.RMSMappingQuality</class>
-      <class>org.broadinstitute.sting.gatk.walkers.annotator.SpanningDeletions</class>
+      <class name="org.broadinstitute.sting.gatk.walkers.annotator.AlleleBalance" />
+      <class name="org.broadinstitute.sting.gatk.walkers.annotator.DepthOfCoverage" />
+      <class name="org.broadinstitute.sting.gatk.walkers.annotator.HomopolymerRun" />
+      <class name="org.broadinstitute.sting.gatk.walkers.annotator.MappingQualityZero" />
+      <class name="org.broadinstitute.sting.gatk.walkers.annotator.QualByDepth" />
+      <class name="org.broadinstitute.sting.gatk.walkers.annotator.RMSMappingQuality" />
+      <class name="org.broadinstitute.sting.gatk.walkers.annotator.SpanningDeletions" />
     </dependencies>
   </executable>
 </package>
diff --git a/packages/VariantEval.xml b/packages/VariantEval.xml
index 720b5f56e..4960725f1 100644
--- a/packages/VariantEval.xml
+++ b/packages/VariantEval.xml
@@ -1,12 +1,10 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<package>
-  <name>VariantEval</name>
-  <executable>
-    <name>VariantEval</name>
-    <main-class>org.broadinstitute.sting.gatk.CommandLineGATK</main-class>
-    <properties>StingText.properties</properties>
+<package name="VariantEval">
+  <executable name="VariantEval">
+    <main-class name="org.broadinstitute.sting.gatk.CommandLineGATK" />
+    <resource-bundle file="StingText.properties" />
     <dependencies>
-      <class>org.broadinstitute.sting.playground.gatk.walkers.varianteval.VariantEvalWalker</class>
+      <class name="org.broadinstitute.sting.playground.gatk.walkers.varianteval.VariantEvalWalker" />
     </dependencies>
   </executable>
 </package>
diff --git a/packages/VariantFiltration.xml b/packages/VariantFiltration.xml
index 317a050b8..e137cf00c 100644
--- a/packages/VariantFiltration.xml
+++ b/packages/VariantFiltration.xml
@@ -1,13 +1,11 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<package>
-  <name>VariantFiltration</name>
-  <executable>
-    <name>VariantFiltration</name>
-    <main-class>org.broadinstitute.sting.gatk.CommandLineGATK</main-class>
-    <properties>StingText.properties</properties>
+<package name="VariantFiltration">
+  <executable name="VariantFiltration">
+    <main-class name="org.broadinstitute.sting.gatk.CommandLineGATK" />
+    <resource-bundle file="StingText.properties" />
     <dependencies>
       <!-- Variant filtration -->
-      <class>org.broadinstitute.sting.gatk.walkers.filters.VariantFiltrationWalker</class>
+      <class name="org.broadinstitute.sting.gatk.walkers.filters.VariantFiltrationWalker" />
     </dependencies>
   </executable>
 </package>