# HG changeset patch
# User stef
# Date 1409129995 14400
# Node ID cc5254dac2b6a3116ebd13918b5b67de2cccf671

Uploaded

diff -r 000000000000 -r cc5254dac2b6 QDNAseq.R
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/QDNAseq.R	Wed Aug 27 04:59:55 2014 -0400
@@ -0,0 +1,520 @@
+#!/usr/bin/Rscript
+
+## --------------------
+## prints all arguments as msg
+## --------------------
+catMsg <- function( msg=c() ){	
+	cat( MAIN_NAME, paste( msg, collapse="" ), "\n", sep='')
+}
+## --------------------
+## return the location of this script
+## --------------------
+getScriptPath <- function(){
+    cmd.args <- commandArgs()
+    m <- regexpr("(?<=^--file=).+", cmd.args, perl=TRUE)
+    script.dir <- dirname(regmatches(cmd.args, m))
+    if( length(script.dir) == 0 ) stop("[ERR] Can't determine script dir: please call the script with Rscript\n")
+    if( length(script.dir) > 1 ) stop("[ERR] Can't determine script dir: more than one '--file' argument detected\n")
+    return(script.dir)
+}
+## --------------------
+## Some html creation functions
+## --------------------
+htmlTableRow <- function( string_array=c() ){
+	td_cells <- ''
+	for ( i in string_array ){ 
+		td_cells <- paste( td_cells, '<td>', i, '</td>', sep='' )	
+	}
+	return( paste( "<tr>", td_cells, "</tr>") )
+}
+htmlLink <- function( path, desc="LINK" ){
+	return( paste( '<a href="', path, '">', desc, "</a>", sep='') )
+}
+## --------------------
+## constructs a list with input bam file info
+## --------------------
+makeBamFileList <- function( paths, names ){	
+	tmp <- list()
+	l1 <- length(paths)
+	l2 <- length(names)
+	if ( l1 != l2 ) stop( "Unequal amount of bam-paths (", l1, ") and -names (", l2, ") in makeBamFileList!!!\n" )
+	for ( i in 1:length(paths) ){
+		path <- paths[i]
+		name <- names[i]
+		file <- basename(path)
+
+		tmp[[ file ]] <- name
+		tmp[[ 'all_paths' ]] <- c( tmp[[ 'all_paths' ]], path )
+		tmp[[ 'all_files' ]] <- c( tmp[[ 'all_files' ]], file )
+		tmp[[ 'all_names' ]] <- c( tmp[[ 'all_names' ]], name )
+	}
+	return( tmp )
+}
+
+## --------------------
+## copied code for extracting the regions by segment call status
+## --------------------
+fuseRegions <- function( obj, minRatio=0 ) {
+	if ( ncol(obj) > 1 ) stop('Please specify which sample...')
+
+	data <- data.frame( obj@featureData@data[,1:3], copynumber(obj), segmented(obj), check.names=FALSE, stringsAsFactors=FALSE)
+	colnames( data ) <- c( "chr", "start", "end", "log2", "segmentval" )
+	
+	fused.data <- data.frame()
+	curr.bin <- 1
+	for ( chr in unique( data$chr ) ) {
+		chr.data  <- data[ data$chr == chr, ]
+		prev.bin  <- curr.bin
+		prev.log2 <- chr.data[ 1, 'log2' ]
+		prev.segm <- chr.data[ 1, 'segmentval' ]
+		start     <- chr.data[ 1, 'start' ]
+
+		if ( nrow(chr.data) > 1) {
+			for ( i in 2:nrow(chr.data) ) {
+				curr.bin  <- curr.bin + 1
+				curr.segm <- chr.data[ i, 'segmentval']
+
+				if ( curr.segm != prev.segm ) {
+					fused.data <- rbind( fused.data, data.frame( chr=chr, start=start, end=chr.data[ i-1, 'end'], segmentval=round(prev.segm, digits=DECIMALS) ) )
+					prev.segm <- curr.segm
+					prev.bin  <- curr.bin
+					start     <- chr.data[ i, 'start']
+				}
+			}
+			fused.data <- rbind( fused.data, data.frame( chr=chr, start=start, end=chr.data[ i-1, 'end'], segmentval=round(prev.segm, digits=DECIMALS) ) )
+		}else{
+			fused.data <- rbind( fused.data, data.frame( chr=chr, start=start, end=chr.data[ i-1, 'end'], segmentval=round(prev.segm, digits=DECIMALS) ) )
+		}
+	}
+	## remove regions with low amplitude
+	fused.data <- fused.data[ abs(fused.data$segmentval) >= minRatio, ]
+	fused.data
+}
+
+## DESC: takes the output of fuse.regions and outputs a txt file per sample
+outputRegionsFromList <- function ( regionsList, outputBasename, outputDir="./", binSize, storeList ){
+	if ( missing(regionsList) ) stop( 'Please provide regionsList...' )
+	if ( missing(outputBasename) ) stop( 'Please provide outputBasename...' )
+	if ( !is.list(regionsList) ) stop( 'Input not a list...?' )
+	if ( length(regionsList) < 1 ) stop( 'List seems empty...?' )
+	if ( file.exists( outputDir ) ) catMsg( c(" Using dir ", outputDir, " for output") )
+	else dir.create( outputDir )
+
+	## have to set R output options otherwise scientific method is used at some point
+	options( "scipen"=100 )
+
+	sampleCount <- length( regionsList )
+	sampleNames <- names( regionsList )
+	bedgraphColumns <- c( 'chr', 'start', 'end', 'segmentval' )
+	
+	catMsg( c( " There are ", sampleCount, " samples found in input list") )
+
+	for ( sample in sampleNames ){		
+		catMsg( c(" Working on sample ", sample ) )
+		regionCount <- nrow( regionsList[[sample]] )
+		
+		outSampleBase   <- paste( outputBasename, '_', sample, '_', binSize, 'kbp', sep='')
+		outBedgraphFile <- paste( outSampleBase, '.bedGraph', sep="" )
+		outBedgraphPath <- paste( outputDir, '/', outBedgraphFile, sep="" )
+
+		## ---------- BEDGRAPH ----------
+		txt <- paste( "track type=bedGraph color=0,100,0 altColor=255,0,0 name=", sample," description=segmented_regions_from_QDNAseq_",binSize,"kbp\n", sep="")
+		sink( outBedgraphPath )
+			cat( txt )
+		sink()
+		write.table( regionsList[[sample]][,bedgraphColumns], outBedgraphPath, quote=F, sep="\t", row.names=F, append=T, col.names=F)
+		#outFiles[[sample]] <- c( outBedgraphFile )
+		storeList[[ paste( binSize, sample, 'bedgraph', sep="_")]] <- outBedgraphFile
+	}
+	return(storeList)
+}
+
+
+## ==================================================
+## Start of analysis
+## ==================================================
+MAIN_NAME <- '[INFO] '
+TOOL_PATH <- getScriptPath()
+CSS_FILE  <- paste( TOOL_PATH, '/static/css/QDNAseq.css', sep="" )
+DECIMALS  <- 3
+WEB_LINK  <- 'http://www.bioconductor.org/packages/release/bioc/html/QDNAseq.html'
+PURE_CSS  <- 'http://yui.yahooapis.com/pure/0.5.0/pure-min.css'
+
+catMsg( "Starting QDNAseq wrapper" )	
+catMsg( "Loading R libraries" )
+suppressWarnings( suppressMessages( library( QDNAseq, quietly = TRUE ) ) )
+suppressWarnings( suppressMessages( library( CGHcall, quietly = TRUE ) ) )
+
+## only one param: the tmp config file
+cmdLineArgs <- commandArgs(TRUE)
+config      <- cmdLineArgs[1]
+
+## sourcing the config file will load all input params
+## many variables are imported via sourced "config"
+source( config )
+
+## desparate tries to make png text scale well, damn you R...!
+PLOT_RES  <- min( PLOT_WIDTH, PLOT_HEIGHT ) / 6.3 
+#PLOT_PS <- min( PLOT_WIDTH, PLOT_HEIGHT ) / 40
+#TXT_FACTOR <- PLOT_WIDTH/480
+#PAR_SET   <- list( pch=22, cex.lab=TXT_FACTOR, cex.main=TXT_FACTOR )
+PAR_SET   <- list( pch=22 )
+
+systemUser <- system("whoami",T)
+qdnaseqVersion <- packageDescription( "QDNAseq" )$Version
+rVersion <- R.version.string
+startTime <- Sys.time()
+analysisStart <- as.character( startTime )
+catMsg( c("QDNAseq version: ", qdnaseqVersion) )
+catMsg( c( rVersion ) )
+
+## get the comma separated list of chromosomes to exclude
+excludeChrs <- unlist( strsplit( excludeChrsString, ",") )
+binSizes <- as.numeric( unlist( strsplit( binSizesString, ",") ) )
+
+
+## ------------------------
+## DEBUG
+if ( debug ){
+	catMsg( c("Analysis run under user: ", systemUser ) )
+	catMsg( c("Here comes sessionInfo: " ) )
+	print( sessionInfo() )
+}
+## /DEBUG
+## ------------------------
+
+## prepare output dir
+if ( !file.exists( outputPath) ){
+	dir.create( outputPath )
+}
+
+## copy source config file to output dir to include it in output zip
+file.copy( config, paste(outputPath, 'galaxyConfigFile.R', sep='/') )
+
+## setup bam filelist for easy retrieval later
+fileList    <- makeBamFileList( bamsPaths, bamsNames )
+bamCount    <- length( fileList[[ 'all_paths' ]] )
+
+gzipOutputName <- paste( 'QDNAseqResults_', outputName, '.zip', sep='' )
+gzipOutputPath <- paste( outputPath, '/', gzipOutputName, sep='')
+htmlOutputName <- 'index.html'
+htmlOutputPath <- paste( outputPath, '/', htmlOutputName, sep='')
+
+plotted_images <- list() # to keep track of images for later linking
+regions <- list() # will contain the segments
+outputFiles <- list()
+
+## ------------------------
+## in case of debug just use inbuilt LGG data for speedup
+if ( debug ){ 
+	binSizes <- c(15)
+	bamsPaths  <- c( "BUILD_IN_DATA")
+	bamsNames  <- c( "LGG150")
+	fileList   <- makeBamFileList( bamsPaths, bamsNames )
+	bamCount   <- length( fileList[[ 'all_paths' ]] )
+}
+
+for ( binSize in binSizes ){
+
+	## ------------------------
+	## construct output file-names and -paths
+	## ------------------------
+	robjReadCoName <- paste( binSize, 'kbp_QDNAseqReadCounts.rds', sep='')
+	robjCopyNrName <- paste( binSize, 'kbp_QDNAseqCopyNumbers.rds', sep='')
+	igvCopyNrName  <- paste( binSize, 'kbp_QDNAseqCopyNumbers.igv', sep='')
+	robjSegmntName <- paste( binSize, 'kbp_QDNAseqCopyNumbersSegmented.rds', sep='')
+	regiOutputName <- paste( binSize, 'kbp_QDNAseqRegions.rds', sep='')
+	noiseImgName   <- paste( binSize, 'kbp_QDNAseqNoiseplot.png', sep='')
+	
+	robjReadCoPath <- paste( outputPath, '/', robjReadCoName, sep='')
+	robjCopyNrPath <- paste( outputPath, '/', robjCopyNrName, sep='')
+	robjSegmntPath <- paste( outputPath, '/', robjSegmntName, sep='')
+	robjRegionPath <- paste( outputPath, '/', regiOutputName, sep='')
+	igvCopyNrPath  <- paste( outputPath, '/', igvCopyNrName, sep='')
+	noiseImgPath   <- paste( outputPath, '/', noiseImgName, sep='')
+
+	binAnnotations <- getBinAnnotations( binSize=binSize, type=experimentType )
+
+	## in case of debug just use inbuilt LGG data for speedup
+	if ( debug ){
+		data(LGG150)
+		readCounts <- LGG150
+	}else{
+		## provide bamnames because in galaxy everyting is called "dataset_###"
+		readCounts <- binReadCounts( binAnnotations, bamfiles=fileList[[ 'all_paths' ]], bamnames=fileList[[ 'all_names' ]] )	
+	}
+
+	readCountsFiltered    <- applyFilters( readCounts, residual=TRUE, blacklist=filterBlacklistedBins, mappability=mappabilityCutoff, chromosomes=excludeChrs )
+	readCountsFiltered    <- estimateCorrection( readCountsFiltered )
+	copyNumbers           <- correctBins( readCountsFiltered )
+	copyNumbersNormalized <- normalizeBins( copyNumbers )
+	copyNumbersSmooth     <- smoothOutlierBins( copyNumbersNormalized )
+	sampleNames           <- readCountsFiltered@phenoData@data$name
+
+	## save objects to output dir
+	saveRDS( readCountsFiltered, robjReadCoPath );
+	saveRDS( copyNumbersSmooth, robjCopyNrPath );
+	exportBins( copyNumbersSmooth, file=igvCopyNrPath, format="igv" )
+
+	## also save objects for galaxy history output if requested
+	if ( doOutputCopynumbersIgv ){
+		#@ a bit hacky galaxy way to allow an unknown number of output files based on param selection
+		#@ see: https://wiki.galaxyproject.org/Admin/Tools/Multiple%20Output%20Files
+		historyName <- paste(binSize, 'kbp-IGV', sep="")
+		igvFile <- paste( newFilePath, "/primary_", outputId, "_", historyName, "_visible_txt", sep="" )
+		exportBins( copyNumbersSmooth, file=igvFile, format="igv" )
+		catMsg( c("Exported igv file to history for ", binSize, "kbp bin") )
+	}
+
+	## proceed with calling if requested
+	if ( doSegment ){
+		copyNumbersSegmented  <- segmentBins( copyNumbersSmooth, undo.splits=undoSplits, undo.SD=undoSD )
+		copyNumbersSegmented  <- normalizeSegmentedBins( copyNumbersSegmented )
+		cgh <- makeCgh( copyNumbersSegmented )
+		saveRDS( copyNumbersSegmented, robjSegmntPath );
+	}
+
+	## ------------------------
+	## create output files
+	## ------------------------
+	png( noiseImgPath, width=PLOT_HEIGHT, height=PLOT_HEIGHT, res=PLOT_RES );
+		par( PAR_SET )
+		noisePlot( readCountsFiltered, main=paste( "Noise Plot ", binSize, "kbp", sep=''), col="darkgreen" )
+	dev.off()
+
+	binSize <- as.character( binSize ) # to avoid R using it as array index... (*#$^@ you R!)
+	binSizeString <- paste( binSize, 'kbp', sep='')
+
+	for (i in 1:length(sampleNames) ){
+		
+		sample <- sampleNames[i]
+		usedReads  <- readCountsFiltered@phenoData@data$used.reads[i]
+		catMsg( c("Creating plots for sample: ", sample, " (", binSizeString, ")" ) )	
+
+		type <- 'CopyNumbers'
+		img_file <- paste( sample, '_', binSize, 'kbp_QDNAseq', type, '.png',  sep='')
+		img_file_path <- paste( outputPath, '/', img_file, sep='' )
+
+		## COPYNUMBER PLOT
+		png( img_file_path, width=PLOT_WIDTH, height=PLOT_HEIGHT, res=PLOT_RES ); 
+			par( PAR_SET )
+			plot( copyNumbersSmooth[ ,sample ], main=paste(sample, ": CopyNumbers", sep="") ) 
+			mtext( paste( binSizeString, " bins", sep=""), 3 )
+			abline( h=c(-2,-1,1,2,3,4), lty=1, lwd=0.5, col="grey" )
+		dev.off()
+		
+		plotted_images[[ paste(binSize, sample, type, sep="_" ) ]] <- img_file
+		
+		if ( doSegment ){
+			type <- 'Segmented'
+			img_file <- paste( sample, '_', binSize, 'kbp_QDNAseq', type, '.png',  sep='')
+			img_file_path <- paste( outputPath, '/', img_file, sep='' )
+			
+			## COPYNUMBER PLOT
+			png( img_file_path, width=PLOT_WIDTH, height=PLOT_HEIGHT, res=PLOT_RES ); 
+				par( PAR_SET )
+				plot( copyNumbersSegmented[ ,sample ], main=paste(sample, ": CopyNumbers and Segments", sep="") )
+				mtext( paste( "(", binSizeString, " bins)", sep=""), 3 )
+				abline( h=c(-2,-1,1,2,3,4), lty=1, lwd=0.5, col="grey" )
+			dev.off()
+
+			plotted_images[[ paste(binSize, sample, type, sep="_" ) ]] <- img_file
+
+			catMsg( c(" Fusing regions of sample: ", sample) )
+			regions[[ sample ]] <- fuseRegions( cgh[, sample] )
+
+			region_count <- nrow( data.frame( regions[[ sample ]] ) )
+			catMsg( c( ' sample "', sample, '" has ', region_count, " regions" ) )
+			plotted_images[[ paste(binSize, sample, 'region_count', sep="_" ) ]] <- region_count
+		}
+		
+		## add USED read counts
+		plotted_images[[ paste(binSize, sample, 'usedReads', sep="_" ) ]] <- usedReads
+	}
+
+	if ( doSegment ){
+		saveRDS( regions, robjRegionPath )
+		plotted_images <- outputRegionsFromList( regions, outputBasename=outputName, outputDir=outputPath, binSize=binSize, storeList=plotted_images )	
+	}
+}# end bin
+
+
+## ----- debug -----
+#catMsg( "done" )
+#q(status=0)
+## ---- /debug -----
+
+
+## ------------------------
+## prepare output
+## ------------------------
+catMsg( "...zipping output")
+zip_cmd <- paste( "zip -j", gzipOutputPath, paste(outputPath,'/*',sep='') ) ## -j is for removing dirs from the tree
+system( zip_cmd )
+
+## ------------------------
+## get filesizes for report
+## ------------------------
+zippedSize <- paste( round( file.info( gzipOutputPath )[["size"]] / 1e+6, digits=2 ), 'MB' )
+endTime <- Sys.time()
+timeDiff <- format( round( endTime - startTime, 3 ) )
+analysisEnd <- as.character( endTime )
+
+## ------------------------
+## creating html output to be linked to from the middle galaxy pane
+## ------------------------
+sink( file = htmlOutputPath, type = "output" )
+		cat( "<html>\n")
+		cat( "<head>\n")
+
+			cat( "\t", '<title>QDNAseq Report | ', outputName,'</title>', "\n", sep='' )
+			cat( "\t", '<link rel="stylesheet" href="', PURE_CSS, '">', "\n", sep='' )
+			cat( "\t<style>\n", sep='')
+				## include CSS into html file, makes it more portable
+				cat( "\t\t", readLines( CSS_FILE ), sep="\n\t\t" )
+				#cat( "\t\th1 {color:red;}", "\n")
+			cat( "\n\t</style>\n" )
+			
+		cat( "\n</head>\n")
+		cat( "\n<body>\n")
+
+		cat( "<h1>QDNAseq Report</h1>", "\n")
+		
+		cat( '<h3 class="qdnaseq">About this analysis</h3>', "\n")
+		cat( '<p>This page provides access to all results. To have a local copy of this report just download the <a href="', gzipOutputName, '" class="button">zipfile</a> with all output (', zippedSize, ')</p>', "\n", sep='')		
+		
+		## ------------------------
+		## table with general info
+		## ------------------------
+		cat( '<h3 class="qdnaseq">Settings</h3><p>', "\n")
+		cat( '<table class="pure-table pure-table-striped"><tbody>' )
+			cat( htmlTableRow( c( "AnalysisName", outputName ) ) )
+			cat( htmlTableRow( c( "AnalysisStart", analysisStart ) ) )
+			cat( htmlTableRow( c( "AnalysisEnd", analysisEnd ) ) )
+			cat( htmlTableRow( c( "AnalysisTime", timeDiff ) ) )
+			cat( htmlTableRow( c( "BinSizes (kbp)", paste(binSizes,collapse=", ") ) ) )
+			cat( htmlTableRow( c( "R info", rVersion ) ) )
+			cat( htmlTableRow( c( "QDNAseq info", qdnaseqVersion ) ) )
+			
+			sampleStrings <- c()
+			for ( galaxyName in fileList[[ 'all_files' ]] ){
+				sampleName <- fileList[[ galaxyName ]]
+				sampleStrings <- c( sampleStrings, paste( galaxyName, ' (', sampleName, ')', sep='' ) )
+			}
+			cat( htmlTableRow( c( "InputBams", paste( sampleStrings, collapse=", ") ) ) )
+
+		cat( "</tbody></table></p>", "\n")
+		
+		## ------------------------
+		## list with links to all output files
+		## ------------------------
+		cat( '<h3 class="qdnaseq">Output files</h3><p>', "\n")
+		cat( '<p>This table contains output files that can be used for local downstream analysis with the bioconductor QDNAseq package. For each bin-size / data-level there is a R data structure file with data of all samples. See ', htmlLink( WEB_LINK, 'the bioconductor QDNAseq documentation' ), ' for more information on how to work with these files</p>', "\n", sep='')
+		cat( '<table class="pure-table pure-table-striped">', "\n" )
+		cat( '<thead><th>Type</th>', as.vector( mapply( paste, "<th>", binSizes, "kbp</th>", sep="" ) ),'</thead>', "\n" )
+		cat( "<tbody>", "\n")
+			files <- list()
+			fileTypes <- c( 'ReadCounts.rds', 'CopyNumbers.rds' )
+			if ( doSegment ){ fileTypes <- c( fileTypes, 'CopyNumbersSegmented.rds') }
+
+			for ( fileType in fileTypes ){
+				fileNames <- mapply( paste, binSizes, paste( 'kbp_QDNAseq', fileType, sep=''), sep='')
+				fileLinks <- mapply( htmlLink, fileNames, paste( binSizes, "kbp", sep="" ) )
+				cat( htmlTableRow( c( fileType, fileLinks ) ) )	
+			}
+		cat( "\n</tbody></table></p>", "\n")
+
+		## ------------------------
+		## table with links to files	
+		## ------------------------
+		ratio <- PLOT_WIDTH / PLOT_HEIGHT
+		width <- 960; height <- width / ratio ## bigger img
+		width_t <- 100; height_t <- 40 ## thumb img
+
+		cat( '<h3 class="qdnaseq">Results: overview</h3><p>', "\n")
+		cat( '<p>This table contains the visual results of the copy number aberration analysis. You can click on an image to jump to the larger version. If segmentation was performed as well the number of segments is shown and a file with genomic regions can be downloaded (just remember to inspect the results carefully as this is a more exprimental step).</p>', "\n", sep='')
+		plots_html <- ''
+
+		colspan <- 1
+		binHeader <- "<th>Image</th>"
+		if ( doSegment ){ # extra column with segment info
+			colspan <- 2 
+			binHeader <- "<th>Image</th><th>Segments</th>"
+		} 
+		cat( '<table class="pure-table pure-table-striped">', "\n" )
+		cat( '<thead><tr><th></th><th></th>', as.vector( mapply( paste, "<th colspan=\"", colspan,"\">", binSizes, "kbp</th>", sep="" ) ), '</tr></thead>' )
+		cat( '<thead><tr><th>Sample / File</th><th>Reads</th>', rep( binHeader, length(binSizes) ), '</tr></thead>' )
+		cat( '<tbody>' )
+
+			for ( bam_file in bamsNames ){
+				
+				usedReads <- plotted_images[[ paste(binSize, bam_file, 'usedReads', sep="_" ) ]]
+				usedReads <- format( as.integer(usedReads), digits=4, decimal.mark=".", big.mark="," )
+				htmlRow <- paste( '<tr><td>', bam_file, '</td><td>', usedReads, '</td>', sep='' )
+
+				for ( binSize in binSizes ){
+					
+					## add thumbnails to table with links to anchors on html page
+					copy_img <- plotted_images[[ paste(binSize, bam_file, 'CopyNumbers', sep="_" ) ]]
+					html_copy_thumb <- htmlLink( path=paste('#', copy_img, sep=''), paste('<img src="',copy_img,'" alt="', bam_file, '" width="', width_t, '" height="', height_t, '">', sep='') )
+					html_copy_img <- htmlLink( path=copy_img, paste('<img id="', copy_img,'" src="',copy_img,'" alt="',bam_file, '" width="', width, '" height="', height, '">', sep='') )
+					html_segm_img <- ''
+					html_bedGraph <- ''
+					region_count <- ''
+					htmlRow <- paste( htmlRow, '<td>', html_copy_thumb, '</td>' )
+
+					if ( doSegment ){
+						segm_img <- plotted_images[[ paste(binSize, bam_file, 'Segmented', sep="_" ) ]]
+						region_count <- plotted_images[[ paste(binSize, bam_file, 'region_count', sep="_" ) ]]
+
+						html_bedGraph <- htmlLink( path=plotted_images[[ paste(binSize, bam_file, 'bedgraph', sep="_" ) ]], 'bedGraph' )
+						html_segm_img <- htmlLink( path=segm_img, paste('<img id="', segm_img,'" src="', segm_img,'" alt="', bam_file, '" width="', width, '" height="', height,'">', sep='') )
+						htmlRow <- paste( htmlRow, '<td>', region_count, ' (', html_bedGraph, ')</td>', sep="" )
+					}
+					plots_html <- paste( plots_html, html_copy_img, "\n", html_segm_img, "\n<br \\>\n", sep='' )	
+				}
+				plots_html <- paste( plots_html, "\n<hr \\>\n", sep='' )
+				## add info to overview table, including small thumbnails
+				htmlRow <- paste( htmlRow, '</tr>', sep='' )
+				cat( htmlRow, "\n" )				
+			}
+		cat( "</tbody></table></p>", "\n")
+		
+		## ------------------------
+		## section with various output shown
+		## ------------------------
+		cat( '<h3 class="qdnaseq">Results: Sample plots</h3><p>', "\n")
+		## now include (large) images in html page
+		cat( plots_html, "\n")
+		cat( "\n</p></body>\n")
+		cat( "\n</html>\n")
+sink()
+
+## ------------------------
+## creating main html output for galaxy history
+## ------------------------
+sink( file = outputHtml, type = "output" )
+		
+		cat( "<head>", "\n")
+			cat( "\t", '<link rel="stylesheet" href="', PURE_CSS, '">', "\n", sep='' )
+
+			cat( "<style>", "\n")
+				## include CSS directly into html file
+				cat( paste( "\t", '/* the css here originates from ', CSS_FILE,' */', "\n") )
+				cat( paste( "\t", readLines( CSS_FILE, n = -1)), sep="\n" )
+			cat( "</style>", "\n")
+		cat( "</head>", "\n")
+
+		cat( '<h1>QDNAseq Results (', outputName,')</h1>', "\n", sep="")
+		cat( '<p>Explore <a href="', htmlOutputName, '" class="button">the results</a> directly within galaxy</p>', "\n", sep="")
+		cat( '<p>Or download a <a href="', gzipOutputName, '" class="button">zipfile</a> with all output (', zippedSize, ')</p>', "\n", sep="" )
+
+sink()
+
+## ------------------------
+## create final zip and quit with status 0 to tell galaxy all was fine
+## ------------------------
+catMsg( "zipping all output")
+system( paste( "zip -j ", gzipOutputPath, paste(outputPath,'/', htmlOutputName, sep='') ) )
+catMsg( "done" )
+q(status=0)
diff -r 000000000000 -r cc5254dac2b6 QDNAseq.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/QDNAseq.xml	Wed Aug 27 04:59:55 2014 -0400
@@ -0,0 +1,291 @@
+<tool id="QDNAseq" name="QDNAseq" version="0.0.2" force_history_refresh="True">
+  
+  <requirements>
+    
+    <!-- R 3.1.0 dependency will be used instead when available, now default R is used, see command -->
+    <!-- <requirement type="package" version="3.1.0">R</requirement> -->
+    <!-- <requirement type="package" version="1.0.5">qdnaseq</requirement> -->
+    <requirement type="package" version="0.1.18">samtools</requirement>
+  </requirements>
+
+  <description>Quantitative copy number abberation detection</description>
+
+  <!-- command block to call script with default R installation -->
+  <!-- change to /full/path/to/Rscript if required (eg /ccagc/lib/R/R-3.1.0/bin/Rscript) -->
+  <command interpreter="Rscript"> 
+    QDNAseq.R 
+    $qdnaseq_cfg
+  </command>
+
+  <stdio>
+    <!-- Anything higher than 0 means the R script didnt finish (correctly) -->
+    <!-- Because different R packages deal with err/warn differently unable to waterproof this -->
+    <exit_code range="1:" level="fatal" description="R script didnt finish correctly, check log" />
+  </stdio>
+  
+  <inputs>
+    
+    <!-- ==================== -->
+    <!-- General inputs -->
+    <!-- ==================== -->
+    
+    <!-- Job name: must contain non-whitespace chars -->
+    <param name="jobName" type="text" optional="false" label="Analysis/ouput name" help="Supply a name for the outputs to remind you what they contain" value="TEST">
+      <validator type="empty_field" />
+      <validator type="regex" message="This field should contain some non-whitespace character">.*\S</validator>
+    </param>
+
+    <!-- Bin Size: only certain sizes are supported by QDNAseq package -->
+    <param name="binSizes" type="select" optional="false" multiple="true" label="Select bin-sizes to use (kb)" help="Larger bin sizes provide faster analysis but lower resolution">
+      <option value="1000" selected="true">1Mb</option>
+      <option value="100">100kb</option>
+      <option value="30">30kb</option>
+      <option value="15">15kb</option>
+      <option value="5">5kb</option>
+      <option value="1">1kb</option>
+    </param>
+
+    <!-- Experiment type: only one type (SR50) supported now, maybe more in the future-->
+    <param name="experimentType" type="select" label="Type of sequencing data" help="Currently only single end reads of lenght 50 are supported within galaxy">
+      <option value="SR50">Single Reads of 50bp</option>
+      <!-- <option value="PE1000">PairedEnd1000</option> -->
+    </param>
+
+    <!-- ==================== -->
+    <!-- Input BAMs -->
+    <!-- ==================== -->
+    <param name="bams" type="data" multiple="true" optional="True" format="bam" label="Input BAMs" help="Select the BAM files to analyze" />
+
+    <!-- ==================== -->
+    <!-- Optional segmenting -->
+    <!-- ==================== -->
+    <param name="doSegment" type="select" label="Also perform segmentation" help="Segmentation collects bins with similar ratio into regions">
+      <option value="TRUE">yes</option>
+      <option value="FALSE">no</option>
+    </param>
+
+    <!-- ==================== -->
+    <!-- Option to use your own bin annotations file -->
+    <!-- ==================== -->
+    <conditional name="binannotations_source">
+      <param name="show" type="select" label="Bin annotations to use" help="Default bin-annotations are for GRCh37/hg19 and tuned for 50bp reads (single end)">
+        <option value="default">Default</option>
+        <option value="history">From history</option>
+      </param>
+      <when value="history">
+        <param name="binannotation_file" type="data" multiple="false" label="R data structure file (*.rds) with bin-annotations" help="If you made your own bin-annotations with the QDNAseq bioconductor package you can upload them to your history and select here" />
+      </when>
+      <when value="default">
+        <param name="binannotation_file" type="hidden" value="" />
+      </when>
+      
+    </conditional> 
+
+    <!-- ==================== -->
+    <!-- Optional advanced options -->
+    <!-- ==================== -->
+    <conditional name="advanced">
+      <param name="show" type="select" label="Use advanced options" help="Select yes to show and use filter and output options">
+        <option value="no">no</option>
+        <option value="yes">yes</option>
+      </param>
+      <when value="yes">
+        
+        <param name="copynumbers_igv" type="select" label="Also output copynumber IGV file to history">
+          <option value="FALSE">no</option>
+          <option value="TRUE">yes</option>
+        </param>
+
+        <param name="undo_splits" type="select" label="undoSplits" help="If set to sdundo, see undoSD below">
+          <option value="sdundo">sdundo</option>
+          <option value="prune">prune</option>
+          <option value="none">none</option>
+        </param>
+
+        <param name="undoSD" size="10" type="float" value="1" label="undoSD" help='The number of SDs between means to keep a split if undo.splits="sdundo".' />
+          
+        <param name="blacklist" type="select" label="Filter blacklisted bins (blacklist)" help="Will exclude all blacklisted bins in the binannotation if set">
+          <option value="TRUE">yes</option>
+          <option value="FALSE">no</option>
+        </param>
+
+        <param name="mappability" type="integer" value="0" min="0" max="100" label="Filter bins with lower mappability" help="Will exclude all bins will lower mappability than this number (0-100)" />
+      
+        <!-- ==================== -->
+        <!-- Optional graphical/plotting options -->
+        <!-- ==================== -->
+        <param name="plot_width" size="3" type="integer" value="1440" label="Width of the png image produced" />
+        <param name="plot_height" size="3" type="integer" value="720" label="Height of the png image produced" />
+        <param name="exclude_chrs" type="select" multiple="true" label="Hide these chromosomes in plots" help="Currently only standard human chromosomes supported. NOTE: other filters might also exclude chromosomes">
+          <option value="1">1</option><option value="2">2</option>
+          <option value="3">3</option><option value="4">4</option>
+          <option value="5">5</option><option value="6">6</option>
+          <option value="7">7</option><option value="8">8</option>
+          <option value="9">9</option><option value="10">10</option>
+          <option value="11">11</option><option value="12">12</option>
+          <option value="13">13</option><option value="14">14</option>
+          <option value="15">15</option><option value="16">16</option>
+          <option value="17">17</option><option value="18">18</option>
+          <option value="19">19</option><option value="20">20</option>
+          <option value="21">21</option><option value="22">22</option>
+          <option value="X" selected="true">X</option>
+          <option value="Y" selected="true">Y</option>
+        </param>
+      </when>
+
+      <!-- need to set defaults because params are passed to R regardless of conditional opened/closed -->
+      <when value="no">
+        <param name="copynumbers_igv" type="hidden" value="FALSE" />
+        <param name="undoSD" type="hidden" value="1" />
+        <param name="undo_splits" type="hidden" value="sdundo" />
+        <param name="blacklist" type="hidden" value="TRUE" />
+        <param name="mappability" type="hidden" value="0" />
+        <param name="plot_width" type="hidden" value="1440" />
+        <param name="plot_height" type="hidden" value="720" />
+        <param name="exclude_chrs" type="hidden" value="X,Y" />
+      </when>
+    </conditional>
+
+    <!-- ==================== -->
+    <!-- Option to perform a test run with built in data -->
+    <!-- ==================== -->
+    <param name="debug" type="select" label="Run with test data" help="Use inbuilt LGG150 data instead of input BAMs">
+      <option value="FALSE">no</option>
+      <option value="TRUE">yes</option>
+    </param>
+    
+  </inputs>
+  <!-- ==================== -->
+  <!-- Config file to pass params to R script -->
+  <!-- ==================== -->
+  <configfiles>
+    <configfile name="qdnaseq_cfg">
+## Desc: this file was sourced in QDNAseq R wrapper script
+##  as means to pass all galaxy params to R
+
+## -----
+## required params
+## -----
+"${binSizes}" -> binSizesString
+"${experimentType}" -> experimentType
+"${jobName}" -> outputName
+
+## -----
+## extra main params
+## -----
+"${htmlFile}" -> outputHtml
+"${htmlFile.id}" -> outputId
+"${__new_file_path__}" -> newFilePath
+
+"${htmlFile.files_path}" -> outputPath
+as.logical( "${doSegment}" ) -> doSegment
+as.logical( "${debug}" ) -> debug
+
+## -----
+## own bin-annotations file options
+## -----
+"${binannotations_source.binannotation_file}" -> binAnnotations
+
+## -----
+## advanced options
+## -----
+as.double( "${advanced.undoSD}" ) -> undoSD
+as.logical( "${advanced.blacklist}" ) -> filterBlacklistedBins
+as.integer( "${advanced.mappability}" ) -> mappabilityCutoff
+"${advanced.undo_splits}" -> undoSplits
+as.logical( "${advanced.copynumbers_igv}" ) -> doOutputCopynumbersIgv
+
+## #for binSize in $binSizes}.split(",")# 
+## "${binSize}kbp_${igvCopyNumbers}" -> copyNumbersIgvDatasetFile
+## #end for
+
+## -----
+## plot options
+## -----
+as.integer( "${advanced.plot_width}" ) -> PLOT_WIDTH
+as.integer( "${advanced.plot_height}" ) -> PLOT_HEIGHT
+"${advanced.exclude_chrs}" -> excludeChrsString
+  
+## -----
+## input BAMs init
+## -----
+c() -> bamsPaths
+c() -> bamsNames
+
+#for bam in $bams# 
+c( bamsPaths, "${bam}" ) -> bamsPaths
+c( bamsNames, "${bam.name}" ) -> bamsNames
+#end for
+
+    </configfile>
+  </configfiles>
+
+  <!-- ==================== -->
+  <!-- Main output is an html based report -->
+  <!-- ==================== -->
+  <outputs>
+
+    <!-- main output is a html report -->
+    <!-- ...but there can be more outputs using the id of the htmlFile output -->
+    <data format="html" name="htmlFile" label="QDNAseq: ${jobName}" />
+
+  </outputs>
+
+  <!-- ==================== -->
+  <!-- Tests still to be done -->
+  <!-- ==================== -->
+
+  <!-- 
+  <tests>
+    <test>
+      <param name="input1" value="input1" />   
+      <param name="input2" value="input2" />   
+    </test>
+  </tests>
+  -->
+
+  <help>
+.. class:: infomark
+
+**Introduction**
+
+This tool is a wrapper for the R Bioconductor package QDNAseq_
+
+.. _QDNAseq: http://www.bioconductor.org/packages/release/bioc/html/QDNAseq.html
+
+It determines the copy number state of human chromosomes 1 - 22 for (shallow coverage) whole genome sequencing data.
+
+For questions/remarks about the galaxy part of this tool, see contact form here_
+
+.. _here: http://www.stefs.nl/wp/contact
+
+You can **test this tool** with built-in data by selecting the option "Run with test data" and press execute.
+
+-----
+
+.. class:: warningmark
+
+As there is no R 3.1.0 galaxy-package yet (a requirement for QDNAseq), the **dependencies** need to be installed by hand and available to the user under which galaxy runs: R (3.1.0) and bioconductor package QDNAseq (>= 1.0.5). In case the default R is not 3.1.0, also the wrapper xml must be updated to include the correct path during installation of this tool.
+
+.. class:: warningmark
+
+The input BAMs are expected to be **single end reads of 50bp length** mapped to GRCh37/hg19 genome build. Other experiment setups are currently not tested or supported within galaxy. See the documentation of QDNAseq at bioconductor on how to deal with different setups (or keep fingers crossed ;) )
+
+.. class:: warningmark
+
+Requires **internet access** for downloading bin-annotations from bitbucket and to show some styling (css) of the final report
+
+-----
+
+**Citation**
+
+For the underlying QDNAseq R package please cite: llari Scheinin, Daoud Sie et al. DNA copy number analysis of fresh and formalin-fixed specimens by whole-genome sequencing: improved correction of systematic biases and exclusion of problematic regions, (submitted). See also the bioconductor package_ documentation.
+
+.. _package: http://www.bioconductor.org/packages/release/bioc/html/QDNAseq.html
+
+.. image:: LGG150_copynumber.png
+.. image:: LGG150_copynumberSegmented.png
+
+  </help>
+
+</tool>
diff -r 000000000000 -r cc5254dac2b6 static/css/QDNAseq.css
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/static/css/QDNAseq.css	Wed Aug 27 04:59:55 2014 -0400
@@ -0,0 +1,6 @@
+/* --- QDNAseq CSS --- */
+body{ padding: 0px 20px; }
+pre { padding: 0px 25px; }
+h3.qdnaseq{ color: #355681;	border-bottom: 1px solid #355681;}
+.marker { background: yellow; color: red;}
+.button { background: rgb(28, 184, 65); color: white; border-radius: 4px; padding: 4px 10px }
diff -r 000000000000 -r cc5254dac2b6 static/images/LGG150_copynumber.png
Binary file static/images/LGG150_copynumber.png has changed
diff -r 000000000000 -r cc5254dac2b6 static/images/LGG150_copynumberSegmented.png
Binary file static/images/LGG150_copynumberSegmented.png has changed
diff -r 000000000000 -r cc5254dac2b6 tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Wed Aug 27 04:59:55 2014 -0400
@@ -0,0 +1,28 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    
+    <package name="samtools" version="0.1.18">
+        <repository changeset_revision="c0f72bdba484" name="package_samtools_0_1_18" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" prior_installation_required="TRUE" />
+    </package>
+
+    <!-- As soon as R 3_1_0 package works, all QDNAseq dependencies will be set via "package_qdnaseq_1_0_5" -->
+    <!-- Now this depency has to be manually installed by installing Bioconductor package "QDNAseq" -->
+    
+    <package name="R" version="3.1.0">
+        <repository changeset_revision="a6cc7706ea14" name="package_r_3_1_0" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" prior_installation_required="TRUE" />
+    </package>
+    
+    <!--
+    <package name="qdnaseq" version="1.0.5">
+        <repository name="package_qdnaseq_1_0_5" owner="stef"/>
+    </package>
+    -->
+
+    <!-- environment variable not in use now -->
+    <!--
+    <action type="set_environment">
+        <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable>
+    </action>
+    -->
+    
+</tool_dependency>