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view java-genomics-toolkit/resources/toolConf.xml @ 0:1daf3026d231

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author timpalpant
date Mon, 13 Feb 2012 21:55:55 -0500
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<?xml version="1.0" encoding="UTF-8"?>
<!-- This is the tool configuration file for the ToolRunner GUI -->
<tools>
	<section name="Converters">
		<tool name="IntervalToWig" class="edu.unc.genomics.converters.IntervalToWig" />
		<tool name="RomanNumeralize" class="edu.unc.genomics.converters.RomanNumeralize" />
	</section>
	
	<section name="NGS">
		<tool name="Autocorrelation" class="edu.unc.genomics.ngs.Autocorrelation" />
		<tool name="BaseAlignCounts" class="edu.unc.genomics.ngs.BaseAlignCounts" />
		<tool name="FindAbsoluteMaxima" class="edu.unc.genomics.ngs.FindAbsoluteMaxima" />
		<tool name="IntervalLengthDistribution" class="edu.unc.genomics.ngs.IntervalLengthDistribution" />
		<tool name="IntervalStats" class="edu.unc.genomics.ngs.IntervalStats" />
		<tool name="PowerSpectrum" class="edu.unc.genomics.ngs.PowerSpectrum" />
		<tool name="RollingReadLength" class="edu.unc.genomics.ngs.RollingReadLength" />
	</section>
	
	<section name="Nucleosomes">
		<tool name="FindBoundaryNucleosomes" class="edu.unc.genomics.nucleosomes.FindBoundaryNucleosomes" />
		<tool name="GreedyCaller" class="edu.unc.genomics.nucleosomes.GreedyCaller" />
		<tool name="MapDyads" class="edu.unc.genomics.nucleosomes.MapDyads" />
		<tool name="NRLCalculator" class="edu.unc.genomics.nucleosomes.NRLCalculator" />
		<tool name="Phasogram" class="edu.unc.genomics.nucleosomes.Phasogram" />
	</section>
	
	<section name="Visualization">
		<tool name="IntervalAverager" class="edu.unc.genomics.visualization.IntervalAverager" />
		<tool name="KMeans" class="edu.unc.genomics.visualization.KMeans" />
		<tool name="MatrixAligner" class="edu.unc.genomics.visualization.MatrixAligner" />
	</section>
	
	<section name="WigMath">
		<tool name="Add" class="edu.unc.genomics.wigmath.Add" />
		<tool name="Average" class="edu.unc.genomics.wigmath.Average" />
		<tool name="Divide" class="edu.unc.genomics.wigmath.Divide" />
		<tool name="GaussianSmooth" class="edu.unc.genomics.wigmath.GaussianSmooth" />
		<tool name="LogTransform" class="edu.unc.genomics.wigmath.LogTransform" />
		<tool name="MovingAverageSmooth" class="edu.unc.genomics.wigmath.MovingAverageSmooth" />
		<tool name="Multiply" class="edu.unc.genomics.wigmath.Multiply" />
		<tool name="Scale" class="edu.unc.genomics.wigmath.Scale" />
		<tool name="Subtract" class="edu.unc.genomics.wigmath.Subtract" />
		<tool name="WigSummary" class="edu.unc.genomics.wigmath.WigSummary" />
		<tool name="ZScore" class="edu.unc.genomics.wigmath.ZScore" />
	</section>
</tools>