--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/galaxyToolConf.xml	Mon Feb 13 22:12:06 2012 -0500
@@ -0,0 +1,41 @@
+<!-- Add to galaxy/tool_conf.xml within the <toolbox></toolbox> section -->
+  <label name="Java Genomics Toolkit" />
+  <section name="Converters" id="java-genomics-toolkit-converters">
+  	<tool file="java-genomics-toolkit/galaxy-conf/IntervalToWig.xml" />
+    <tool file="java-genomics-toolkit/galaxy-conf/RomanNumeralize.xml" />
+  </section>
+  <section name="Nucleosomes" id="java-genomics-toolkit-nucleosomes">
+    <tool file="java-genomics-toolkit/galaxy-conf/FindBoundaryNucleosomes.xml" />
+    <tool file="java-genomics-toolkit/galaxy-conf/GreedyCaller.xml" />
+    <tool file="java-genomics-toolkit/galaxy-conf/MapDyads.xml" />
+    <tool file="java-genomics-toolkit/galaxy-conf/NRLCalculator.xml" />
+    <tool file="java-genomics-toolkit/galaxy-conf/Phasogram.xml" />
+  </section>
+  <section name="NGS" id="java-genomics-toolkit-ngs">
+    <tool file="java-genomics-toolkit/other-tools/Autocorrelation.xml" />
+    <tool file="java-genomics-toolkit/galaxy-conf/BaseAlignCounts.xml" />
+    <tool file="java-genomics-toolkit/galaxy-conf/FindAbsoluteMaxima.xml" />
+    <tool file="java-genomics-toolkit/galaxy-conf/IntervalLengthDistribution.xml" />
+    <tool file="java-genomics-toolkit/galaxy-conf/IntervalStats.xml" />
+    <tool file="java-genomics-toolkit/galaxy-conf/PowerSpectrum.xml" />
+    <tool file="java-genomics-toolkit/galaxy-conf/RollingReadLength.xml" />
+  </section>
+  <section name="WigMath" id="java-genomics-toolkit-wigmath">
+    <tool file="java-genomics-toolkit/galaxy-conf/Add.xml" />
+    <tool file="java-genomics-toolkit/galaxy-conf/Average.xml" />
+    <tool file="java-genomics-toolkit/galaxy-conf/Divide.xml" />
+    <tool file="java-genomics-toolkit/galaxy-conf/GaussianSmooth.xml" />
+    <tool file="java-genomics-toolkit/galaxy-conf/LogTransform.xml" />
+    <tool file="java-genomics-toolkit/galaxy-conf/MovingAverageSmooth.xml" />
+    <tool file="java-genomics-toolkit/galaxy-conf/Multiply.xml" />
+    <tool file="java-genomics-toolkit/galaxy-conf/Scale.xml" />
+    <tool file="java-genomics-toolkit/galaxy-conf/Subtract.xml" />
+    <tool file="java-genomics-toolkit/galaxy-conf/WigSummary.xml" />
+    <tool file="java-genomics-toolkit/galaxy-conf/ZScore.xml" />
+  </section>
+  <section name="Visualization" id="java-genomics-toolkit-visualization">
+    <tool file="java-genomics-toolkit/galaxy-conf/IntervalAverager.xml" />
+    <tool file="java-genomics-toolkit/galaxy-conf/KMeans.xml" />
+    <tool file="java-genomics-toolkit/galaxy-conf/MatrixAligner.xml" />
+    <tool file="java-genomics-toolkit/galaxy-conf/StripMatrix.xml" />
+  </section>
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