--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rnbeads.xml	Sat Apr 20 07:14:22 2013 -0400
@@ -0,0 +1,502 @@
+<?xml version="0.9"?>
+<tool id="rnbeads" name="RnBeads" version="0.9">
+  <description>Performs RnBeads analysis for the selected set of </description>
+  <requirements>
+    <requirement type="set_environment" version="0.9">R_SCRIPTS_PATH</requirement>
+    <requirement type="package" version="3.0.0">R</requirement>
+  </requirements>
+  <command interpreter="bash">rnbeads_galaxy_wrapper.sh  
+      #if str( $inputDataSelector.dataType ) == "idat"  
+      	--data-type="idat.dir"
+      	--pheno="$inputDataSelector.sampleAnnotations"
+      	#if str( $idatSelector.idatSelector.idatSource ) == "history"
+      	--idat-files =="
+      		#for $input_files in $inputDataSelector.input_series:
+    			${input_files.input_files}\t				
+    		#end for
+    	"
+      	#else:
+      		--idat-files == "$idatRepo"
+      	#end if
+      #end if
+      #if str( $inputDataSelector.dataType ) == "gsreport"
+      	--data-type="GS.report"
+      	--gs-report="$inputDataSelector.gsReportFile"
+      #end if
+      #if str( $inputDataSelector.dataType ) == "geo"
+      	--data-type="GEO"
+      	--geo-series=$inputDataSelector.geoSeries
+      #end if
+      #if str( $inputDataSelector.dataType ) == "tables"
+        --data-type="data.files"
+        --pheno="$inputDataSelector.sampleAnnotations"
+      #end if
+      #if str( $inputDataSelector.dataType ) == "tables"
+      	--data-type="data.files"
+      	--pheno="$inputDataSelector.sampleAnnotations"
+      	--betas="$inputDataSelector.betaTable"
+      	--pvals="$inputDataSelector.pvalTable"
+      #end if
+      #if str( $inputDataSelector.dataType ) == "bed"
+        --data-type="bed.dir"
+      	--pheno="$inputDataSelector.sampleAnnotations"
+        --beds =="
+      	#for $input_files in $inputDataSelector.input_series:
+    			${input_files.input_files}\t				
+    		#end for
+      #end if
+      	--report-dir="$html_file.extra_files_path"
+      	--output-file="$html_file"
+      #if str( $options.optionSet ) == "full"
+      					#if str( $options.analysisName ) != ""
+					--analysis-name="$options.analysisName" 
+				#end if
+				#if str( $options.logging ) == "True"
+					--logging
+				#end if
+				#if str( $options.email ) != ""
+					--email="$options.email" 
+				#end if
+				#if str( $options.assembly ) != ""
+					--assembly="$options.assembly" 
+				#end if
+				#if str( $options.analyzeSites ) == "True"
+					--analyze-sites
+				#end if
+				#if str( $options.regionTypes ) != ""
+					--region-types="$options.regionTypes" 
+				#end if
+				#if str( $options.identifiersColumn ) != ""
+					--identifiers-column="$options.identifiersColumn" 
+				#end if
+				#if str( $options.pointsCategory ) != ""
+					--points-category="$options.pointsCategory" 
+				#end if
+				#if str( $options.colorsCategory ) != ""
+					--colors-category="$options.colorsCategory" 
+				#end if
+				#if str( $options.colorsGradient ) != ""
+					--colors-gradient="$options.colorsGradient" 
+				#end if
+				#if str( $options.minGroupSize ) != ""
+					--min-group-size="$options.minGroupSize" 
+				#end if
+				#if str( $options.maxGroupCount ) != ""
+					--max-group-count="$options.maxGroupCount" 
+				#end if
+				#if str( $options.gzLargeFiles ) == "True"
+					--gz-large-files
+				#end if
+				#if str( $options.strandSpecific ) == "True"
+					--strand-specific
+				#end if
+				#if str( $options.replicateIdColumn ) != ""
+					--replicate-id-column="$options.replicateIdColumn" 
+				#end if
+				#if str( $options.loadingNormalization ) == "True"
+					--loading-normalization
+				#end if
+				#if str( $options.loadingDefaultDataType ) != ""
+					--loading-default-data-type="$options.loadingDefaultDataType" 
+				#end if
+				#if str( $options.loadingTableSeparator ) != ""
+					--loading-table-separator="$options.loadingTableSeparator" 
+				#end if
+				#if str( $options.loadingBedStyle ) != ""
+					--loading-bed-style="$options.loadingBedStyle" 
+				#end if
+				#if str( $options.loadingBedColumns ) != ""
+					--loading-bed-columns="$options.loadingBedColumns" 
+				#end if
+				#if str( $options.loadingBedFrameShift ) != ""
+					--loading-bed-frame-shift="$options.loadingBedFrameShift" 
+				#end if
+				#if str( $options.normalizationMethod ) != ""
+					--normalization-method="$options.normalizationMethod" 
+				#end if
+				#if str( $options.normalizationSubtractBackground ) == "True"
+					--normalization-subtract-background
+				#end if
+				#if str( $options.qc ) == "True"
+					--qc
+				#end if
+				#if str( $options.qcBoxplots ) == "True"
+					--qc-boxplots
+				#end if
+				#if str( $options.qcBarplots ) == "True"
+					--qc-barplots
+				#end if
+				#if str( $options.qcNegativeBoxplot ) == "True"
+					--qc-negative-boxplot
+				#end if
+				#if str( $options.qcSnpHeatmap ) == "True"
+					--qc-snp-heatmap
+				#end if
+				#if str( $options.qcSnpBoxplot ) == "True"
+					--qc-snp-boxplot
+				#end if
+				#if str( $options.qcSnpBarplot ) == "True"
+					--qc-snp-barplot
+				#end if
+				#if str( $options.qcSampleBatchSize ) != ""
+					--qc-sample-batch-size="$options.qcSampleBatchSize" 
+				#end if
+				#if str( $options.filteringContextRemoval ) != ""
+					--filtering-context-removal="$options.filteringContextRemoval" 
+				#end if
+				#if str( $options.filteringSnp ) == "True"
+					--filtering-snp
+				#end if
+				#if str( $options.filteringSnpFrequency ) != ""
+					--filtering-snp-frequency="$options.filteringSnpFrequency" 
+				#end if
+				#if str( $options.filteringSnpAccepted ) != ""
+					--filtering-snp-accepted="$options.filteringSnpAccepted" 
+				#end if
+				#if str( $options.filteringSexChromosomesRemoval ) == "True"
+					--filtering-sex-chromosomes-removal
+				#end if
+				#if str( $options.filteringMissingValueQuantile ) != ""
+					--filtering-missing-value-quantile="$options.filteringMissingValueQuantile" 
+				#end if
+				#if str( $options.filteringCoverageThreshold ) != ""
+					--filtering-coverage-threshold="$options.filteringCoverageThreshold" 
+				#end if
+				#if str( $options.filteringLowCoverageMasking ) == "True"
+					--filtering-low-coverage-masking
+				#end if
+				#if str( $options.filteringHighCoverageOutliers ) == "True"
+					--filtering-high-coverage-outliers
+				#end if
+				#if str( $options.filteringGreedycut ) == "True"
+					--filtering-greedycut
+				#end if
+				#if str( $options.filteringGreedycutPvalueThreshold ) != ""
+					--filtering-greedycut-pvalue-threshold="$options.filteringGreedycutPvalueThreshold" 
+				#end if
+				#if str( $options.filteringGreedycutRcTies ) != ""
+					--filtering-greedycut-rc-ties="$options.filteringGreedycutRcTies" 
+				#end if
+				#if str( $options.filteringDeviationThreshold ) != ""
+					--filtering-deviation-threshold="$options.filteringDeviationThreshold" 
+				#end if
+				#if str( $options.batch ) == "True"
+					--batch
+				#end if
+				#if str( $options.batchDreductionColumns ) != ""
+					--batch-dreduction-columns="$options.batchDreductionColumns" 
+				#end if
+				#if str( $options.batchPrincipalComponents ) != ""
+					--batch-principal-components="$options.batchPrincipalComponents" 
+				#end if
+				#if str( $options.batchCorrelationColumns ) != ""
+					--batch-correlation-columns="$options.batchCorrelationColumns" 
+				#end if
+				#if str( $options.batchCorrelationPvalueThreshold ) != ""
+					--batch-correlation-pvalue-threshold="$options.batchCorrelationPvalueThreshold" 
+				#end if
+				#if str( $options.batchCorrelationPermutations ) != ""
+					--batch-correlation-permutations="$options.batchCorrelationPermutations" 
+				#end if
+				#if str( $options.batchCorrelationQc ) == "True"
+					--batch-correlation-qc
+				#end if
+				#if str( $options.profiles ) == "True"
+					--profiles
+				#end if
+				#if str( $options.profilesBetaDistribution ) == "True"
+					--profiles-beta-distribution
+				#end if
+				#if str( $options.profilesIntersample ) == "True"
+					--profiles-intersample
+				#end if
+				#if str( $options.profilesDeviationPlots ) == "True"
+					--profiles-deviation-plots
+				#end if
+				#if str( $options.profilesColumns ) != ""
+					--profiles-columns="$options.profilesColumns" 
+				#end if
+				#if str( $options.profilesClustering ) == "True"
+					--profiles-clustering
+				#end if
+				#if str( $options.profilesClusteringTopProbes ) != ""
+					--profiles-clustering-top-probes="$options.profilesClusteringTopProbes" 
+				#end if
+				#if str( $options.regionProfilesTypes ) != ""
+					--region-profiles-types="$options.regionProfilesTypes" 
+				#end if
+				#if str( $options.differential ) == "True"
+					--differential
+				#end if
+				#if str( $options.differentialPermutations ) != ""
+					--differential-permutations="$options.differentialPermutations" 
+				#end if
+				#if str( $options.differentialComparisonColumns ) != ""
+					--differential-comparison-columns="$options.differentialComparisonColumns" 
+				#end if
+				#if str( $options.differentialEnrichment ) == "True"
+					--differential-enrichment
+				#end if
+				#if str( $options.exportToUcsc ) != ""
+					--export-to-ucsc="$options.exportToUcsc" 
+				#end if
+				#if str( $options.exportToBed ) == "True"
+					--export-to-bed
+				#end if
+				#if str( $options.exportToCsv ) == "True"
+					--export-to-csv
+				#end if
+				#if str( $options.exportTypes ) != ""
+					--export-types="$options.exportTypes" 
+				#end if
+				#if str( $options.colors3Gradient ) != ""
+					--colors-3-gradient="$options.colors3Gradient" 
+				#end if
+				#if str( $options.loggingMemory ) == "True"
+					--logging-memory
+				#end if
+				#if str( $options.usePstoimg ) == "True"
+					--use-pstoimg
+				#end if
+      #end if
+  </command>
+  <inputs>
+    <conditional name="inputDataSelector">
+    	<param name="dataType" type="select" label="Data Type">
+    		<option value="tables">Tabular data</option>
+    		<option value="idats">IDAT files</option>
+    		<option value="gsreport">GenomeStudio report</option>
+    		<option value="geo">Gene Expression Omnibus series</option>		
+    		<option value="bed">BED files</option>
+    	</param>
+    	<when value="tables">
+    		<param name="sampleAnnotations" type="data" format="tabular" label="Sample Annotation File"/>
+    		<param name="betaTable" type="data" format="tabular" label="Table with beta-values"/> 	
+    		<param name="pvalTable" type="data" format="tabular" label="Table with detection p\-values"/>
+    	</when>
+    	<when value="idats">
+    		<param name="sampleAnnotations" type="data" format="tabular" label="Sample Annotation File"/>
+    		<conditional name="idatSelector">
+    			<param name="idatSource" type="select" label="IDAT source">
+    				<option value="history">Select from history</option>
+    				<option value="repo">Repository on the server</option>
+    			</param>
+    			<when value="repo">
+    				<param name="idatRepo" type="select" label="Select an IDAT repository">
+    					<options from_data_table="rnbeads_repos">
+            				<filter type="sort_by" column="2" />
+            				<validator type="no_options" message="No repositories are available" />
+          				</options>
+          			</param>
+    			</when>
+    			<when value="history">
+    				<repeat min="1" name="idatSeries" title="Input IDAT file">
+    					<param name="idatFiles" type="data" format="idat" label="IDAT file"/>
+    				</repeat>
+    			</when>
+    		</conditional>
+    	</when>
+    	<when value="gsreport">
+    		<param name="gsReportFile" type="data" format="tabular" label="GenomeStudio report" />
+    	</when>
+    	<when value="geo">
+    		<param name="geoSeries" type="text" label="GEO series" />
+    	</when>
+    	<when value="bed">
+    		<param name="sampleAnnotations" type="data" format="tabular" label="Sample Annotation File" />
+   				<repeat min="1" name="bedSeries" title="Input BED file">
+    					<param name="idatFiles" type="data" format="idat"/>
+    		    </repeat>    	
+        </when>
+    </conditional>
+    <conditional name="options">
+    	<param name="optionSet" type="select" label="Options Set">
+    		<option value="default">Default options</option>
+    		<option value="full">Full option set</option>
+    	</param>
+    	<when value="default" />
+    	<when value="full">
+ 				<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>
+     	</when>
+    </conditional>
+  </inputs>
+  
+  <outputs>
+	<data format="html" name="html_file" label="index.html" />
+  </outputs>
+
+  <!--
+  <tests>
+    <test>
+      <param name="input" value="fa_gc_content_input.fa"/>
+      <output name="out_file1" file="fa_gc_content_output.txt"/>
+    </test>
+  </tests>  -->
+
+  <help>
+	RnBeads is an R-package for comprehensive analysis of Illumina Infinium HumanMethylation450 BeadChip data. It extends previous approaches for this type of data analysis by high throughput capabilities, as well as presenting results in a comprehensive, highly interpretable fashion.
+  </help>
+
+</tool>
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