galaxyToolConf.xml

<!-- 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/IntervalToBed.xml" />
  	<tool file="java-genomics-toolkit/galaxy-conf/IntervalToWig.xml" />
  	<tool file="java-genomics-toolkit/galaxy-conf/InterpolateDiscontinuousData.xml" />
    <tool file="java-genomics-toolkit/galaxy-conf/RomanNumeralize.xml" />
    <tool file="java-genomics-toolkit/galaxy-conf/GeneTrackToWig.xml" />
    <tool file="java-genomics-toolkit/galaxy-conf/GeneTrackToBedGraph.xml" />
    <tool file="java-genomics-toolkit/galaxy-conf/FastqIlluminaToSanger.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/Phasogram.xml" />
    <tool file="java-genomics-toolkit/galaxy-conf/PercusDecomposition.xml" />
    <tool file="java-genomics-toolkit/galaxy-conf/DynaPro.xml" />
    <tool file="java-genomics-toolkit/galaxy-conf/PairOverlappingNucleosomes.xml" />
  </section>
  <section name="NGS" id="java-genomics-toolkit-ngs">
    <tool file="java-genomics-toolkit/galaxy-conf/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/FindOutlierRegions.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" />
    <tool file="java-genomics-toolkit/galaxy-conf/ReadLengthDistributionMatrix.xml" />
    <tool file="java-genomics-toolkit/galaxy-conf/ExtractDataFromRegion.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/Downsample.xml" />
    <tool file="java-genomics-toolkit/galaxy-conf/FindOutlierRegions.xml" />
    <tool file="java-genomics-toolkit/galaxy-conf/GaussianSmooth.xml" />
    <tool file="java-genomics-toolkit/galaxy-conf/JoinContigs.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/Shift.xml" />
    <tool file="java-genomics-toolkit/galaxy-conf/Subtract.xml" />
    <tool file="java-genomics-toolkit/galaxy-conf/Correlate.xml" />
    <tool file="java-genomics-toolkit/galaxy-conf/Summary.xml" />
    <tool file="java-genomics-toolkit/galaxy-conf/ValueDistribution.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/matrix2png.xml" />
    <tool file="java-genomics-toolkit/galaxy-conf/StripMatrix.xml" />
  </section>
  <section name="DNA Properties" id="java-genomics-toolkit-dnaproperty">
  	<tool file="java-genomics-toolkit/galaxy-conf/DNAPropertyCalculator.xml" />
  	<tool file="java-genomics-toolkit/galaxy-conf/FindNMers.xml" />
  </section>