--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/automated.settings.xml.txt	Sun Apr 21 18:10:16 2013 -0400
@@ -0,0 +1,163 @@
+				<param name="analysisName" type="text"  label="analysis.name, character" value=""/>
+				<param name="logging" type="select" label="logging, logical" value="1">
+					<option value="True">True</option>
+					<option value="False">False</option>
+				</param>
+				<param name="email" type="text"  label="email, character" value=""/>
+				<param name="assembly" type="text"  label="assembly, character" value="hg19"/>
+				<param name="analyzeSites" type="select" label="analyze.sites, logical" value="1">
+					<option value="True">True</option>
+					<option value="False">False</option>
+				</param>
+				<param name="regionTypes" type="text"  label="region.types, character vector" value="tiling,genes,promoters,cpgislands"/>
+				<param name="identifiersColumn" type="text"  label="identifiers.column, character" value=""/>
+				<param name="pointsCategory" type="text"  label="points.category, integer vector" value="16,17,3,15,4,7,8"/>
+				<param name="colorsCategory" type="text"  label="colors.category, character vector" value="#1B9E77,#D95F02,#7570B3,#E7298A,#66A61E,#E6AB02,#A6761D,#666666"/>
+				<param name="colorsGradient" type="text"  label="colors.gradient, character vector" value="#132B43,#56B1F7"/>
+				<param name="minGroupSize" type="text"  label="min.group.size, integer" value="2"/>
+				<param name="maxGroupCount" type="text"  label="max.group.count, integer" value="8"/>
+				<param name="gzLargeFiles" type="select" label="gz.large.files, logical" value="0">
+					<option value="True">True</option>
+					<option value="False">False</option>
+				</param>
+				<param name="strandSpecific" type="select" label="strand.specific, logical" value="0">
+					<option value="True">True</option>
+					<option value="False">False</option>
+				</param>
+				<param name="replicateIdColumn" type="text"  label="replicate.id.column, character" value=""/>
+				<param name="loadingNormalization" type="select" label="loading.normalization, logical" value="1">
+					<option value="True">True</option>
+					<option value="False">False</option>
+				</param>
+				<param name="loadingDefaultDataType" type="text"  label="loading.default.data.type, character" value="idat.dir"/>
+				<param name="loadingTableSeparator" type="text"  label="loading.table.separator, character" value="	"/>
+				<param name="loadingBedStyle" type="text"  label="loading.bed.style, character" value="BisSNP"/>
+				<param name="loadingBedColumns" type="text"  label="loading.bed.columns, integer vector" value="1,2,3,6,4,5"/>
+				<param name="loadingBedFrameShift" type="text"  label="loading.bed.frame.shift, integer" value="1"/>
+				<param name="normalizationMethod" type="text"  label="normalization.method, character" value="illumina"/>
+				<param name="normalizationSubtractBackground" type="select" label="normalization.subtract.background, logical" value="0">
+					<option value="True">True</option>
+					<option value="False">False</option>
+				</param>
+				<param name="qc" type="select" label="qc, logical" value="1">
+					<option value="True">True</option>
+					<option value="False">False</option>
+				</param>
+				<param name="qcBoxplots" type="select" label="qc.boxplots, logical" value="1">
+					<option value="True">True</option>
+					<option value="False">False</option>
+				</param>
+				<param name="qcBarplots" type="select" label="qc.barplots, logical" value="1">
+					<option value="True">True</option>
+					<option value="False">False</option>
+				</param>
+				<param name="qcNegativeBoxplot" type="select" label="qc.negative.boxplot, logical" value="1">
+					<option value="True">True</option>
+					<option value="False">False</option>
+				</param>
+				<param name="qcSnpHeatmap" type="select" label="qc.snp.heatmap, logical" value="1">
+					<option value="True">True</option>
+					<option value="False">False</option>
+				</param>
+				<param name="qcSnpBoxplot" type="select" label="qc.snp.boxplot, logical" value="0">
+					<option value="True">True</option>
+					<option value="False">False</option>
+				</param>
+				<param name="qcSnpBarplot" type="select" label="qc.snp.barplot, logical" value="0">
+					<option value="True">True</option>
+					<option value="False">False</option>
+				</param>
+				<param name="qcSampleBatchSize" type="text"  label="qc.sample.batch.size, integer" value="50"/>
+				<param name="filteringContextRemoval" type="text"  label="filtering.context.removal, character vector" value="CC,CAG,CAH,CTG,CTH,Other"/>
+				<param name="filteringSnp" type="select" label="filtering.snp, logical" value="1">
+					<option value="True">True</option>
+					<option value="False">False</option>
+				</param>
+				<param name="filteringSnpFrequency" type="text"  label="filtering.snp.frequency, double" value="0.01"/>
+				<param name="filteringSnpAccepted" type="text"  label="filtering.snp.accepted, integer" value="2"/>
+				<param name="filteringSexChromosomesRemoval" type="select" label="filtering.sex.chromosomes.removal, logical" value="0">
+					<option value="True">True</option>
+					<option value="False">False</option>
+				</param>
+				<param name="filteringMissingValueQuantile" type="text"  label="filtering.missing.value.quantile, double" value="1"/>
+				<param name="filteringCoverageThreshold" type="text"  label="filtering.coverage.threshold, integer" value="5"/>
+				<param name="filteringLowCoverageMasking" type="select" label="filtering.low.coverage.masking, logical" value="0">
+					<option value="True">True</option>
+					<option value="False">False</option>
+				</param>
+				<param name="filteringHighCoverageOutliers" type="select" label="filtering.high.coverage.outliers, logical" value="0">
+					<option value="True">True</option>
+					<option value="False">False</option>
+				</param>
+				<param name="filteringGreedycut" type="select" label="filtering.greedycut, logical" value="1">
+					<option value="True">True</option>
+					<option value="False">False</option>
+				</param>
+				<param name="filteringGreedycutPvalueThreshold" type="text"  label="filtering.greedycut.pvalue.threshold, double" value="0.05"/>
+				<param name="filteringGreedycutRcTies" type="text"  label="filtering.greedycut.rc.ties, character" value="row"/>
+				<param name="filteringDeviationThreshold" type="text"  label="filtering.deviation.threshold, double" value="0"/>
+				<param name="batch" type="select" label="batch, logical" value="1">
+					<option value="True">True</option>
+					<option value="False">False</option>
+				</param>
+				<param name="batchDreductionColumns" type="text"  label="batch.dreduction.columns, integer vector" value=""/>
+				<param name="batchPrincipalComponents" type="text"  label="batch.principal.components, integer" value="8"/>
+				<param name="batchCorrelationColumns" type="text"  label="batch.correlation.columns, integer vector" value=""/>
+				<param name="batchCorrelationPvalueThreshold" type="text"  label="batch.correlation.pvalue.threshold, double" value="0.01"/>
+				<param name="batchCorrelationPermutations" type="text"  label="batch.correlation.permutations, integer" value="10000"/>
+				<param name="batchCorrelationQc" type="select" label="batch.correlation.qc, logical" value="1">
+					<option value="True">True</option>
+					<option value="False">False</option>
+				</param>
+				<param name="profiles" type="select" label="profiles, logical" value="1">
+					<option value="True">True</option>
+					<option value="False">False</option>
+				</param>
+				<param name="profilesBetaDistribution" type="select" label="profiles.beta.distribution, logical" value="1">
+					<option value="True">True</option>
+					<option value="False">False</option>
+				</param>
+				<param name="profilesIntersample" type="select" label="profiles.intersample, logical" value="1">
+					<option value="True">True</option>
+					<option value="False">False</option>
+				</param>
+				<param name="profilesDeviationPlots" type="select" label="profiles.deviation.plots, logical" value="0">
+					<option value="True">True</option>
+					<option value="False">False</option>
+				</param>
+				<param name="profilesColumns" type="text"  label="profiles.columns, integer vector" value=""/>
+				<param name="profilesClustering" type="select" label="profiles.clustering, logical" value="1">
+					<option value="True">True</option>
+					<option value="False">False</option>
+				</param>
+				<param name="profilesClusteringTopProbes" type="text"  label="profiles.clustering.top.probes, integer vector" value="1000"/>
+				<param name="regionProfilesTypes" type="text"  label="region.profiles.types, character vector" value="genes,promoters,cpgislands"/>
+				<param name="differential" type="select" label="differential, logical" value="1">
+					<option value="True">True</option>
+					<option value="False">False</option>
+				</param>
+				<param name="differentialPermutations" type="text"  label="differential.permutations, integer" value="0"/>
+				<param name="differentialComparisonColumns" type="text"  label="differential.comparison.columns, integer vector" value=""/>
+				<param name="differentialEnrichment" type="select" label="differential.enrichment, logical" value="0">
+					<option value="True">True</option>
+					<option value="False">False</option>
+				</param>
+				<param name="exportToUcsc" type="text"  label="export.to.ucsc, character vector" value="bigBed,bigWig"/>
+				<param name="exportToBed" type="select" label="export.to.bed, logical" value="1">
+					<option value="True">True</option>
+					<option value="False">False</option>
+				</param>
+				<param name="exportToCsv" type="select" label="export.to.csv, logical" value="0">
+					<option value="True">True</option>
+					<option value="False">False</option>
+				</param>
+				<param name="exportTypes" type="text"  label="export.types, character vector" value="sites"/>
+				<param name="colors3Gradient" type="text"  label="colors.3.gradient, character vector" value="#832424,#FFFFFF,#3A3A98"/>
+				<param name="loggingMemory" type="select" label="logging.memory, logical" value="0">
+					<option value="True">True</option>
+					<option value="False">False</option>
+				</param>
+				<param name="usePstoimg" type="select" label="use.pstoimg, logical" value="0">
+					<option value="True">True</option>
+					<option value="False">False</option>
+				</param>