# HG changeset patch
# User iuc
# Date 1508949437 14400
# Node ID 49788db492f71a250b0f8b54e83b58e06b4bbe3e

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7

diff -r 000000000000 -r 49788db492f7 CoverageReport.pl
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CoverageReport.pl	Wed Oct 25 12:37:17 2017 -0400
@@ -0,0 +1,851 @@
+#!/usr/bin/env perl
+# load modules
+use warnings;
+use Getopt::Std;
+use File::Basename;
+use Number::Format;
+use Cwd;
+
+my %opts;
+
+# number format
+my $de = new Number::Format(-thousands_sep =>',',-decimal_point => '.');
+
+##########
+## opts ##
+##########
+## input files
+# b : path to input (b)am file
+# t : path to input (t)arget regions in BED format
+## output files
+# o : report pdf (o)utput file
+## entries in the report
+# r : Coverage per (r)egion (boolean)
+# s : (s)ubregion coverage if average < specified (plots for positions along target region) (boolean)
+# S : (S)ubregion coverage for ALL failed exons  => use either s OR S or you will have double plots. 
+# A : (A)ll exons will be plotted. 
+# L : (L)ist failed exons instead of plotting
+# m : (m)inimal Coverage threshold
+# f : fraction of average as threshold
+# n : sample (n)ame.
+ 
+
+getopts('b:t:o:rsSALm:n:f:', \%opts) ;
+
+my $tmp = getcwd();
+# make output directory in (tmp) working dir
+our $wd = "$tmp/Coverage.".int(rand(1000));
+while (-d $wd) {
+	$wd = "$tmp/Coverage.".int(rand(1000));
+}
+system("mkdir $wd");
+
+## variables
+our %commandsrun = ();
+my ($thresh,$frac,$pdffile,$samplename,$totalmapped);
+
+
+if (!exists($opts{'b'}) || !-e $opts{'b'}) {
+	die('Bam File not found');
+}
+if (!exists($opts{'t'}) || !-e $opts{'t'}) {
+	die('Target File (BED) not found');
+}
+
+if (exists($opts{'m'})) {
+	$thresh = $opts{'m'};
+}
+else {
+	$thresh = 40;
+}
+
+if (exists($opts{'f'})) {
+	$frac = $opts{'f'};
+}
+else {
+	$frac = 0.2;
+}
+
+if (exists($opts{'o'})) {
+	$pdffile = $opts{'o'};
+}
+else {
+	$pdffile = "$wd/CoverageReport.pdf";
+}
+
+
+# 1. Global Summary => default
+&GlobalSummary($opts{'b'}, $opts{'t'});
+
+# 2. Coverage per position
+&SubRegionCoverage($opts{'b'}, $opts{'t'});
+our %filehash;
+if (exists($opts{'s'}) || exists($opts{'S'}) || exists($opts{'A'}) || exists($opts{'L'})) {
+	system("mkdir $wd/SplitFiles");
+	## get position coverages
+	## split input files
+	open IN, "$wd/Targets.Position.Coverage";
+	my $fileidx = 0;
+	my $currreg = '';
+	while (<IN>) {
+		my $line = $_;
+		chomp($line);
+		my @p = split(/\t/,$line);
+		my $reg = $p[0].'-'.$p[1].'-'.$p[2]; #.$p[3];
+		my $ex = $p[3];
+		if ($reg ne $currreg) {
+			## new exon open new outfile
+			if ($currreg ne '') {
+				## filehandle is open. close it
+				close OUT; 
+			}
+			if (!exists($filehash{$reg})) {
+				$fileidx++;
+				$filehash{$reg}{'idx'} = $fileidx;
+				$filehash{$reg}{'exon'} = $ex;
+				open OUT, ">> $wd/SplitFiles/File_$fileidx.txt";
+				$currreg = $reg;
+			}
+			else {
+				open OUT, ">> $wd/SplitFiles/File_".$filehash{$reg}{'idx'}.".txt";
+				$currreg = $reg;
+			}
+		}
+		## print the line to the open filehandle. 	
+		print OUT "$line\n";
+	}
+	close OUT;
+	close IN;
+
+}
+
+## sort output files according to targets file
+if (exists($opts{'r'}) ) {
+	my %hash = ();
+	open IN, "$wd/Targets.Global.Coverage";
+	while (<IN>) {
+            chomp;
+            my @p = split(/\t/,$_) ;
+            $hash{$p[3]} = $_;
+	}
+	close IN;
+	open OUT, ">$wd/Targets.Global.Coverage";
+	open IN, $opts{'t'};
+	while (<IN>) {
+            chomp;
+            my @p = split(/\t/,$_) ;
+            print OUT $hash{$p[3]} . "\n";
+	}
+	close IN;
+	close OUT;
+}
+
+
+####################################
+## PROCESS RESULTS & CREATE PLOTS ##
+####################################
+system("mkdir $wd/Report");
+
+system("mkdir $wd/Rout");
+system("mkdir $wd/Plots");
+
+$samplename = $opts{'n'};
+$samplename =~ s/_/\\_/g;
+$samplename =~ s/\..+$//g;
+
+# 0. Preamble
+## compose preamble
+open OUT, ">$wd/Report/Report.tex";
+print OUT '\documentclass[a4paper,10pt]{article}'."\n";
+print OUT '\usepackage[left=2cm,top=1.5cm,right=1.5cm,bottom=2.5cm,nohead]{geometry}'."\n";
+print OUT '\usepackage{longtable}'."\n";
+print OUT '\usepackage{fancyhdr}'."\n";
+print OUT '\usepackage{fontspec}' . "\n";
+print OUT '\usepackage{color}'."\n";
+print OUT '\definecolor{grey}{RGB}{160,160,160}'."\n";
+print OUT '\definecolor{darkgrey}{RGB}{100,100,100}'."\n";
+print OUT '\definecolor{red}{RGB}{255,0,0}'."\n";
+print OUT '\definecolor{orange}{RGB}{238,118,0}'."\n";
+print OUT '\setlength\LTleft{0pt}'."\n";
+print OUT '\setlength\LTright{0pt}'."\n";
+print OUT '\begin{document}'."\n";
+print OUT '\pagestyle{fancy}'."\n";
+print OUT '\fancyhead{}'."\n";
+print OUT '\renewcommand{\footrulewidth}{0.4pt}'."\n";
+print OUT '\renewcommand{\headrulewidth}{0pt}'."\n";
+print OUT '\fancyfoot[R]{\today\hspace{2cm}\thepage\ of \pageref{endofdoc}}'."\n";
+print OUT '\fancyfoot[C]{}'."\n";
+print OUT '\fancyfoot[L]{Coverage Report for ``'.$samplename.'"}'."\n";
+print OUT '\let\oldsubsubsection=\subsubsection'."\n";
+print OUT '\renewcommand{\subsubsection}{%'."\n";
+print OUT '  \filbreak'."\n";
+print OUT '  \oldsubsubsection'."\n";
+print OUT '}'."\n";
+# main title
+print OUT '\section*{Coverage Report for ``'.$samplename.'"}'."\n";
+close OUT; 
+
+# 1. Summary Report
+# Get samtools flagstat summary of BAM file	
+my $flagstat = `samtools flagstat $opts{'b'}`;
+my @s = split(/\n/,$flagstat);
+# Get number of reads mapped in total 
+## updated on 2012-10-1 !!
+$totalmapped = $s[2];
+$totalmapped =~ s/^(\d+)(\s.+)/$1/;
+
+if ( not $totalmapped){
+    exit;
+}
+
+# count columns
+my $head = `head -n 1 $wd/Targets.Global.Coverage`;
+chomp($head);
+my @cols = split(/\t/,$head);
+my $nrcols = scalar(@cols);
+my $covcol = $nrcols - 3;
+# get min/max/median/average coverage => values
+my $covs = `cut -f $covcol $wd/Targets.Global.Coverage`;
+my @coverages = split(/\n/,$covs);
+my ($eavg,$med,$min,$max,$first,$third,$ontarget) = arraystats(@coverages);
+my $spec = 0;
+$spec=sprintf("%.1f",($ontarget / $totalmapped)*100);
+# get min/max/median/average coverage => boxplot in R
+open OUT, ">$wd/Rout/boxplot.R";
+print OUT 'coverage <- read.table("../Targets.Global.Coverage",as.is=TRUE,sep="\t",header=FALSE)'."\n";
+print OUT 'coverage <- coverage[,'.$covcol.']'."\n";
+print OUT 'png(file="../Plots/CoverageBoxPlot.png", bg="white", width=240, height=480)'."\n";
+print OUT 'boxplot(coverage,range=1.5,main="Target Region Coverage")'."\n";
+print OUT 'graphics.off()'."\n";
+close OUT;
+system("cd $wd/Rout && Rscript boxplot.R") == 0 || die "Could not run boxplot.R with following error '$!'\n";
+
+## global nt coverage plot
+## use perl to make histogram (lower memory)
+open IN, "$wd/Targets.Position.Coverage";
+my %dens;
+my $counter = 0;
+my $sum = 0;
+my $avg = 0;
+
+while (<IN>) {
+	chomp();
+	my @p = split(/\t/);
+	$sum += $p[-1];
+	$counter++;
+	if (defined($dens{$p[-1]})) {
+		$dens{$p[-1]}++;
+	}
+	else {
+		$dens{$p[-1]} = 1;
+	}
+}
+$avg = $sum/$counter;
+close IN;
+open OUT, ">$wd/Rout/hist.txt";
+if (!defined($dens{'0'})) {
+	$dens{'0'} = 0;
+}
+foreach (keys(%dens)) {
+	print OUT "$_;$dens{$_}\n";
+}
+close OUT;
+open OUT, ">$wd/Rout/ntplot.R";
+# read coverage hist in R to plot
+print OUT 'coverage <- read.table("hist.txt" , as.is = TRUE, header=FALSE,sep=";")'."\n";
+print OUT 'mincov <- '."$thresh \n";
+print OUT "avg <- round($avg,digits=8)\n";
+print OUT "colnames(coverage) <- c('cov','count')\n";
+print OUT 'coverage$cov <- coverage$cov / avg'."\n";
+print OUT 'rep <- which(coverage$cov > 1)'."\n";
+print OUT 'coverage[coverage$cov > 1,1] <- 1'."\n";
+print OUT 'values <- coverage[coverage$cov < 1,]'."\n";
+print OUT 'values <- rbind(values,c(1,sum(coverage[coverage$cov == 1,"count"])))'."\n";
+print OUT 'values <- values[order(values$cov),]'."\n";
+print OUT 'prevcount <- 0'."\n";
+# make cumulative count data frame
+print OUT 'for (i in rev(values$cov)) {'."\n";
+print OUT '  values[values$cov == i,"count"] <- prevcount + values[values$cov == i,"count"]'."\n";
+print OUT '  prevcount <- values[values$cov == i,"count"]'."\n";
+print OUT '}'."\n";
+print OUT 'values$count <- values$count / (values[values$cov == 0,"count"] / 100)'."\n";
+# get some values to plot lines.
+print OUT 'mincov.x <- mincov/avg'."\n";
+print OUT 'if (mincov/avg <= 1) {'."\n";
+print OUT '  ii <- which(values$cov == mincov.x)'."\n";
+print OUT '  if (length(ii) == 1) {'."\n";
+print OUT '    mincov.y <- values[ii[1],"count"]'."\n";
+print OUT '  } else {'."\n";
+print OUT '    i1 <- max(which(values$cov < mincov.x))'."\n";
+print OUT '    i2 <- min(which(values$cov > mincov.x))'."\n";
+print OUT '    mincov.y <- ((values[i2,"count"] - values[i1,"count"])/(values[i2,"cov"] - values[i1,"cov"]))*(mincov.x - values[i1,"cov"]) + values[i1,"count"]'."\n";
+print OUT '  }'."\n";
+print OUT '}'."\n";
+# open output image and create plot
+print OUT 'png(file="../Plots/CoverageNtPlot.png", bg="white", width=540, height=480)'."\n";
+print OUT 'par(xaxs="i",yaxs="i")'."\n";
+print OUT 'plot(values$cov,values$count,ylim=c(0,100),pch=".",main="Cumulative Normalised Base-Coverage Plot",xlab="Normalizalised Coverage",ylab="Cumulative Nr. Of Bases")'."\n";
+print OUT 'lines(values$cov,values$count)'."\n";
+print OUT 'if (mincov.x <= 1) {'."\n";
+print OUT '  lines(c(mincov.x,mincov.x),c(0,mincov.y),lty=2,col="darkgreen")'."\n";
+print OUT '  lines(c(0,mincov.x),c(mincov.y,mincov.y),lty=2,col="darkgreen")'."\n";
+print OUT '  text(1,(95),pos=2,col="darkgreen",labels="Threshold: '.$thresh.'x")'."\n";
+print OUT '  text(1,(91),pos=2,col="darkgreen",labels=paste("%Bases: ",round(mincov.y,2),"%",sep=""))'."\n";
+print OUT '} else {'."\n";
+print OUT '  text(1,(95),pos=2,col="darkgreen",labels="Threshold ('.$thresh.'x) > Average")'."\n";
+print OUT '  text(1,(91),pos=2,col="darkgreen",labels="Plotting impossible")'."\n";
+print OUT '}'."\n";
+print OUT 'frac.x <- '."$frac\n";
+print OUT 'ii <- which(values$cov == frac.x)'."\n";
+print OUT 'if (length(ii) == 1) {'."\n";
+print OUT '  frac.y <- values[ii[1],"count"]'."\n";
+print OUT '} else {'."\n";
+print OUT '  i1 <- max(which(values$cov < frac.x))'."\n";
+print OUT '  i2 <- min(which(values$cov > frac.x))'."\n";
+print OUT '  frac.y <- ((values[i2,"count"] - values[i1,"count"])/(values[i2,"cov"] - values[i1,"cov"]))*(frac.x - values[i1,"cov"]) + values[i1,"count"]'."\n";
+print OUT '}'."\n";
+print OUT 'lines(c(frac.x,frac.x),c(0,frac.y),lty=2,col="red")'."\n";
+print OUT 'lines(c(0,frac.x),c(frac.y,frac.y),lty=2,col="red")'."\n";
+#iprint OUT 'text((frac.x+0.05),(frac.y - 2),pos=4,col="red",labels=paste(frac.x," x Avg.Cov : ",round(frac.x * avg,2),"x",sep="" ))'."\n";
+#print OUT 'text((frac.x+0.05),(frac.y-5),pos=4,col="red",labels=paste("%Bases: ",round(frac.y,2),"%",sep=""))'."\n";
+print OUT 'text(1,86,pos=2,col="red",labels=paste(frac.x," x Avg.Cov : ",round(frac.x * avg,2),"x",sep="" ))'."\n";
+print OUT 'text(1,82,pos=2,col="red",labels=paste("%Bases: ",round(frac.y,2),"%",sep=""))'."\n";
+
+print OUT 'graphics.off()'."\n";
+
+close OUT;
+system("cd $wd/Rout && Rscript ntplot.R") == 0 || die "Could not run ntplot.R with following error '$!'\n";
+## PRINT TO .TEX FILE
+open OUT, ">>$wd/Report/Report.tex";
+# average coverage overviews
+print OUT '\subsection*{Overall Summary}'."\n";
+print OUT '{\small ';
+# left : boxplot
+print OUT '\begin{minipage}{0.3\linewidth}\centering'."\n";
+print OUT '\includegraphics[width=\textwidth,keepaspectratio=true]{../Plots/CoverageBoxPlot.png}'."\n";
+print OUT '\end{minipage}'."\n";
+# right : cum.cov.plot
+print OUT '\hspace{0.6cm}'."\n";
+print OUT '\begin{minipage}{0.65\linewidth}\centering'."\n";
+print OUT '\includegraphics[width=\textwidth,keepaspectratio=true]{../Plots/CoverageNtPlot.png}'."\n";
+print OUT '\end{minipage} \\\\'."\n";
+## next line
+print OUT '\begin{minipage}{0.48\linewidth}'."\n";
+print OUT '\vspace{-1.2em}'."\n";
+print OUT '\begin{tabular}{ll}'."\n";
+# bam statistics
+print OUT '\multicolumn{2}{l}{\textbf{\underline{Samtools Flagstat Summary}}} \\\\'."\n";
+foreach (@s) {
+	$_ =~ m/^(\d+)\s(.+)$/;
+	my $one = $1;
+	my $two = $2;
+	$two =~ s/\s\+\s0\s//;
+	$two = ucfirst($two);
+	$one =~ s/%/\\%/g;
+	# remove '+ 0 ' from front
+	$two =~ s/\+\s0\s//;
+	# remove trailing from end
+	$two =~ s/(\s\+.*)|(:.*)/\)/;
+	$two =~ s/%/\\%/g;
+	$two =~ s/>=/\$\\ge\$/g;
+	$two = ucfirst($two);
+	print OUT '\textbf{'.$two.'} & '.$one.' \\\\'."\n";
+}
+print OUT '\end{tabular}\end{minipage}'."\n";
+print OUT '\hspace{1.5cm}'."\n";
+# target coverage statistics
+print OUT '\begin{minipage}{0.4\linewidth}'."\n";
+#print OUT '\vspace{-4.8em}'."\n";
+print OUT '\begin{tabular}{ll}'."\n";
+print OUT '\multicolumn{2}{l}{\textbf{\underline{Target Region Coverage}}} \\\\'."\n";
+print OUT '\textbf{Number of Target Regions} & '.scalar(@coverages).' \\\\'."\n";
+print OUT '\textbf{Minimal Region Coverage} & '.$min.' \\\\'."\n";
+print OUT '\textbf{25\% Region Coverage} & '.$first.' \\\\'. "\n";
+print OUT '\textbf{50\% (Median) Region Coverage} & '.$med.' \\\\'. "\n";
+print OUT '\textbf{75\% Region Coverage} & '.$third.' \\\\'. "\n";
+print OUT '\textbf{Maximal Region Coverage} & '.$max.' \\\\'. "\n";
+print OUT '\textbf{Average Region Coverage} & '.int($eavg).' \\\\'. "\n";
+print OUT '\textbf{Mapped On Target} & '.$spec.' \\\\'."\n";
+print OUT '\multicolumn{2}{l}{\textbf{\underline{Target Base Coverage }}} \\\\'."\n";
+print OUT '\textbf{Number of Target Bases} & '.$counter.' \\\\'."\n";
+print OUT '\textbf{Average Base Coverage} & '.int($avg).' \\\\'. "\n";
+print OUT '\textbf{Non-Covered Bases} & '.$dens{'0'}.' \\\\'."\n";
+#print OUT '\textbf{Bases Covered $ge$ '.$frac.'xAvg.Cov} & '.
+print OUT '\end{tabular}\end{minipage}}'."\n";
+close OUT;
+
+# 2. GLOBAL COVERAGE OVERVIEW PER GENE
+my @failedexons;
+my @allexons;
+my @allregions;
+my @failedregions;
+if (exists($opts{'r'}) || exists($opts{'s'}) || exists($opts{'S'})) {
+	# count columns
+	my $head = `head -n 1 $wd/Targets.Global.Coverage`;
+	chomp($head);
+	my @cols = split(/\t/,$head);
+	my $nrcols = scalar(@cols);
+	my $covcol = $nrcols - 3;
+	# Coverage Plots for each gene => barplots in R, table here.
+	open IN, "$wd/Targets.Global.Coverage";
+	my $currgroup = '';
+	my $startline = 0;
+	my $stopline = 0;
+	my $linecounter = 0;
+	my $nrcol=0;
+	while (<IN>) {
+		$linecounter++;
+		chomp($_);
+		my @c = split(/\t/,$_);
+		push(@allregions,$c[0].'-'.$c[1].'-'.$c[2]);
+		my $group = $c[3];
+		## coverage failure?
+		if ($c[$nrcol-1] < 1 || $c[$covcol-1] < $thresh) {
+			push(@failedexons,$group);
+			push(@failedregions,$c[0].'-'.$c[1].'-'.$c[2]);
+		}
+		## store exon
+		push(@allexons,$group);
+		## extract and check gene
+		$group =~ s/^(\S+)[\|\s](.+)/$1/;
+
+                my $scale;
+		if ($group ne $currgroup ) {
+		    if ($currgroup ne '') {
+			# new gene, make plot. 
+			open OUT, ">$wd/Rout/barplot.R";
+			print OUT 'coveragetable <- read.table("../Targets.Global.Coverage",as.is=TRUE,sep="\t",header=FALSE)'."\n";
+			print OUT 'coverage <- coveragetable[c('.$startline.':'.$stopline.'),'.$covcol.']'."\n";
+			print OUT 'entries <- coveragetable[c('.$startline.':'.$stopline.'),4]'."\n";
+			print OUT 'entries <- sub("\\\\S+\\\\|","",entries,perl=TRUE)'."\n";
+			print OUT 'coverage[coverage < 1] <- 1'."\n";
+			print OUT 'colors <- c(rep("grey",length(coverage)))'."\n";
+			# coverage not whole target region => orange
+			print OUT 'covperc <- coveragetable[c('.$startline.':'.$stopline.'),'.$nrcols.']'."\n";
+			print OUT 'colors[covperc<1] <- "orange"'."\n";
+			# coverage below threshold => red
+			print OUT 'colors[coverage<'.$thresh.'] <- "red"'."\n";
+
+			if ($stopline - $startline > 20) {
+				$scale = 2;
+			}
+			else {
+				$scale = 1;
+			}
+			my $width = 480 * $scale;
+			my $height = 240 * $scale;
+			print OUT 'png(file="../Plots/Coverage_'.$currgroup.'.png", bg="white", width='.$width.', height='.$height.')'."\n";
+			print OUT 'ylim = c(0,max(max(log10(coverage),log10('.($thresh+20).'))))'."\n";
+			print OUT 'mp <- barplot(log10(coverage),col=colors,main="Exon Coverage for '.$currgroup.'",ylab="Log10(Coverage)",ylim=ylim)'."\n";
+			print OUT 'text(mp, log10(coverage) + '.(0.4/$scale).',format(coverage),xpd = TRUE,srt=90)'."\n";
+			print OUT 'text(mp,par("usr")[3]-0.05,labels=entries,srt=45,adj=1,xpd=TRUE)'."\n";
+			print OUT 'abline(h=log10('.$thresh.'),lwd=4,col=rgb(255,0,0,100,maxColorValue=255))'."\n";
+			print OUT 'graphics.off()'."\n";
+			close OUT;
+			system("cd $wd/Rout && Rscript barplot.R") == 0 || die "Could not run barplot.R with following error '$!'\n";
+			if ($scale == 1) {
+				push(@small,'\includegraphics[width=\textwidth,keepaspectratio=true]{../Plots/Coverage_'.$currgroup.'.png}');
+			}
+			else {
+				push(@large,'\includegraphics[width=\textwidth,keepaspectratio=true]{../Plots/Coverage_'.$currgroup.'.png}');
+			}
+
+		    }
+		    $currgroup = $group;
+		    $startline = $linecounter;
+		}
+		$stopline = $linecounter;
+	}
+	close IN;
+	if ($currgroup ne '') {
+		# last gene, make plot. 
+		open OUT, ">$wd/Rout/barplot.R";
+		print OUT 'coveragetable <- read.table("../Targets.Global.Coverage",as.is=TRUE,sep="\t",header=FALSE)'."\n";
+		print OUT 'coverage <- coveragetable[c('.$startline.':'.$stopline.'),'.$covcol.']'."\n";
+		print OUT 'entries <- coveragetable[c('.$startline.':'.$stopline.'),4]'."\n";
+		print OUT 'entries <- sub("\\\\S+\\\\|","",entries,perl=TRUE)'."\n";
+		print OUT 'coverage[coverage < 1] <- 1'."\n";
+		print OUT 'colors <- c(rep("grey",length(coverage)))'."\n";
+		print OUT 'colors[coverage<'.$thresh.'] <- "red"'."\n";
+
+		if ($stopline - $startline > 20) {
+			$scale = 2;
+		}
+		else {
+			$scale = 1;
+		}
+		my $width = 480 * $scale;
+		my $height = 240 * $scale;
+		print OUT 'png(file="../Plots/Coverage_'.$currgroup.'.png", bg="white", width='.$width.', height='.$height.')'."\n";
+		print OUT 'ylim = c(0,max(max(log10(coverage),log10('.($thresh+20).'))))'."\n";
+		print OUT 'mp <- barplot(log10(coverage),col=colors,main="Exon Coverage for '.$currgroup.'",ylab="Log10(Coverage)", ylim=ylim)'."\n";
+		print OUT 'text(mp, log10(coverage) + log10(2),format(coverage),xpd = TRUE,srt=90)'."\n";
+		print OUT 'text(mp,par("usr")[3]-0.1,labels=entries,srt=45,adj=1,xpd=TRUE)'."\n";
+		print OUT 'abline(h=log10('.$thresh.'),lwd=4,col=rgb(255,0,0,100,maxColorValue=255))'."\n";
+		print OUT 'graphics.off()'."\n";
+		close OUT;
+		system("cd $wd/Rout && Rscript barplot.R") == 0 || die "Could not run barplot.R with following error '$!'\n";
+		if ($scale == 1) {
+			push(@small,'\includegraphics[width=\textwidth,keepaspectratio=true]{../Plots/Coverage_'.$currgroup.'.png}');
+		}
+		else {
+			push(@large,'\includegraphics[width=\textwidth,keepaspectratio=true]{../Plots/Coverage_'.$currgroup.'.png}');
+		}
+	}
+	## print to TEX
+	open OUT, ">>$wd/Report/Report.tex";
+	print OUT '\subsection*{Gene Summaries}'."\n";
+	print OUT '\underline{Legend:} \\\\'."\n";
+	print OUT '{\color{red}\textbf{RED:} Coverage did not reach set threshold of '.$thresh.'} \\\\'."\n";
+	print OUT '{\color{orange}\textbf{ORANGE:} Coverage was incomplete for the exon. Overruled by red.} \\\\' ."\n";
+	my $col = 1;
+	foreach (@small) {
+		if ($col > 2) {
+			$col = 1;
+			print OUT "\n";
+		}
+		print OUT '\begin{minipage}{0.5\linewidth}\centering'."\n";
+		print OUT $_."\n";
+		print OUT '\end{minipage}'."\n";
+		$col++;
+	}
+	## new line 
+	if ($col == 2) {
+		print OUT '\\\\'." \n";
+	}
+	foreach(@large) {
+		print OUT $_."\n";
+	}
+	close OUT;
+	
+}
+
+# 3. Detailed overview of failed exons (globally failed)
+if (exists($opts{'s'})) {
+	# count columns
+	my $head = `head -n 1 $wd/Targets.Position.Coverage`;
+	chomp($head);
+        my $subtitle;
+	my @cols = split(/\t/,$head);
+	my $nrcols = scalar(@cols);
+	my $covcol = $nrcols;
+	my $poscol = $nrcols -1;
+	# tex section header
+	open TEX, ">>$wd/Report/Report.tex";
+	print TEX '\subsection*{Failed Exon Plots}'."\n";
+	$col = 1;
+	print TEX '\underline{NOTE:} Only exons with global coverage $<$'.$thresh.' or incomplete coverage were plotted \\\\'."\n";
+	foreach(@failedregions) {
+		if ($col > 2) {
+			$col = 1;
+			print TEX "\n";
+		}
+		# which exon
+		my $region = $_;
+		my $exon = $filehash{$region}{'exon'};
+		# link exon to tmp file
+		my $exonfile = "$wd/SplitFiles/File_".$filehash{$region}{'idx'}.".txt";
+		## determine transcript orientation and location
+		my $firstline = `head -n 1 $exonfile`;
+		my @firstcols = split(/\t/,$firstline);
+		my $orient = $firstcols[5];
+		my $genomicchr = $firstcols[0];
+		my $genomicstart = $firstcols[1];
+		my $genomicstop = $firstcols[2];
+		if ($orient eq '+') {
+			$bps = $genomicstop - $genomicstart + 1;
+			$subtitle = "Region 0-$bps: $genomicchr:".$de->format_number($genomicstart)."+".$de->format_number($genomicstop);
+		}
+		else {
+			$bps = $genomicstop - $genomicstart + 1;
+			$subtitle = "Region 0-$bps: $genomicchr:".$de->format_number($genomicstart)."-".$de->format_number($genomicstop);
+		}
+		# print Rscript
+		open OUT, ">$wd/Rout/exonplot.R";
+		print OUT 'coveragetable <- read.table("'.$exonfile.'",as.is=TRUE,sep="\t",header=FALSE)'."\n";
+		print OUT 'coverage <- coveragetable[,'.$covcol.']'."\n";
+		print OUT 'coverage[coverage < 1] <- 1'."\n";
+		print OUT 'positions <- coveragetable[,'.$poscol.']'."\n";
+		
+		my $width = 480 ;
+		my $height = 240 ;
+		my $exonstr = $exon;
+		$exonstr =~ s/\s/_/g;
+		$exon =~ s/_/ /g;
+		$exon =~ s/\|/ /g;
+		print OUT 'png(file="../Plots/Coverage_'.$exonstr.'.png", bg="white", width='.$width.', height='.$height.')'."\n";
+		print OUT 'ylim = c(0,log10(max(max(coverage),'.($thresh+10).')))'."\n";
+		if ($orient eq '-') {
+			print OUT 'plot(positions,log10(coverage),type="n",main="Coverage for '.$exon.'",ylab="log10(Coverage)",ylim=ylim,xlab="Position",xlim=rev(range(positions)),sub="(Transcribed from minus strand)")'."\n";
+			print OUT 'mtext("'.$subtitle.'")'."\n";
+		}
+		else {
+			print OUT 'plot(positions,log10(coverage),type="n",main="Coverage for '.$exon.'",ylab="log10(Coverage)",ylim=ylim,xlab="Position",sub="(Transcribed from plus strand)")'."\n";
+			print OUT 'mtext("'.$subtitle.'")'."\n";
+		}
+		print OUT 'lines(positions,log10(coverage))'."\n";
+		print OUT 'abline(h=log10('.$thresh.'),lwd=4,col=rgb(255,0,0,100,maxColorValue=255))'."\n";
+		print OUT 'failedpos <- positions[coverage<'.$thresh.']'."\n";
+		print OUT 'failedcov <- coverage[coverage<'.$thresh.']'."\n";
+		print OUT 'points(failedpos,log10(failedcov),col="red",pch=19)'."\n";
+		print OUT 'graphics.off()'."\n";
+		close OUT;
+		# run R script
+		system("cd $wd/Rout && Rscript exonplot.R")== 0 || die "Could not run exonplot.R with following error '$!'\n";
+		# Add to .TEX
+		print TEX '\begin{minipage}{0.5\linewidth}\centering'."\n";
+		print TEX '\includegraphics[width=\textwidth,keepaspectratio=true]{../Plots/Coverage_'.$exonstr.'.png}'."\n";
+		print TEX '\end{minipage}'."\n";
+		$col++;
+	}
+}
+
+## plot failed (subregion) or all exons
+if (exists($opts{'S'}) || exists($opts{'A'})) {
+	# count columns
+	my $head = `head -n 1 $wd/Targets.Position.Coverage`;
+	chomp($head);
+	my @cols = split(/\t/,$head);
+	my $nrcols = scalar(@cols);
+	my $covcol = $nrcols;
+	my $poscol = $nrcols -1;
+	# tex section header
+	open TEX, ">>$wd/Report/Report.tex";
+	print TEX '\subsection*{Failed Exon Plots}'."\n";
+	if (exists($opts{'S'})) {
+		print TEX '\underline{NOTE:} ALL exons were tested for local coverage $<$'.$thresh.' \\\\'."\n";
+	}
+	elsif (exists($opts{'A'})) {
+		print TEX '\underline{NOTE:} ALL exons are plotted, regardless of coverage \\\\'."\n";
+	}
+	$col = 1;
+	foreach(@allregions) {
+		if ($col > 2) {
+			$col = 1;
+			print TEX "\n";
+		}
+		# which exon
+		my $region = $_;
+		my $exon = $filehash{$region}{'exon'};
+		# grep exon to tmp file
+		my $exonfile = "$wd/SplitFiles/File_".$filehash{$region}{'idx'}.".txt";
+		## determine transcript orientation.
+                my $firstline = `head -n 1 $exonfile`;
+                my @firstcols = split(/\t/,$firstline);
+                my $orient = $firstcols[5];
+		my $genomicchr = $firstcols[0];
+		my $genomicstart = $firstcols[1];
+		my $genomicstop = $firstcols[2];
+                my $subtitle;
+                
+		if ($orient eq '+') {
+			my $bps = $genomicstop - $genomicstart + 1;
+			$subtitle = "Region 0-$bps: $genomicchr:".$de->format_number($genomicstart)."+".$de->format_number($genomicstop);
+
+		}
+		else {
+			my $bps = $genomicstop - $genomicstart + 1;
+			$subtitle = "Region 0-$bps: $genomicchr:".$de->format_number($genomicstart)."-".$de->format_number($genomicstop);
+
+		}
+
+		# check if failed
+		if (exists($opts{'S'})) {
+			my $cs = `cut -f $covcol '$exonfile' `;
+			my @c = split(/\n/,$cs);
+			@c = sort { $a <=> $b } @c;
+			if ($c[0] >= $thresh) {
+				# lowest coverage > threshold => skip
+				next;
+			}
+		}
+		# print Rscript
+		open OUT, ">$wd/Rout/exonplot.R";
+		print OUT 'coveragetable <- read.table("'.$exonfile.'",as.is=TRUE,sep="\t",header=FALSE)'."\n";
+		print OUT 'coverage <- coveragetable[,'.$covcol.']'."\n";
+		print OUT 'coverage[coverage < 1] <- 1'."\n";
+		print OUT 'positions <- coveragetable[,'.$poscol.']'."\n";
+		my $width = 480 ;
+		my $height = 240 ;
+		my $exonstr = $exon;
+		$exonstr =~ s/\s/_/g;
+		$exon =~ s/_/ /g;
+		$exon =~ s/\|/ /g;
+		print OUT 'png(file="../Plots/Coverage_'.$exonstr.'.png", bg="white", width='.$width.', height='.$height.')'."\n";
+		print OUT 'ylim = c(0,log10(max(max(coverage),'.($thresh+10).')))'."\n";
+		if ($orient eq '-') {
+			print OUT 'plot(positions,log10(coverage),type="n",main="Coverage for '.$exon.'",ylab="log10(Coverage)",ylim=ylim,xlab="Position",xlim=rev(range(positions)),sub="(Transcribed from minus strand)")'."\n";
+			print OUT 'mtext("'.$subtitle.'")'."\n";
+                }
+                else {
+			print OUT 'plot(positions,log10(coverage),type="n",main="Coverage for '.$exon.'",ylab="log10(Coverage)",ylim=ylim,xlab="Position",sub="(Transcribed from plus strand)")'."\n";
+			print OUT 'mtext("'.$subtitle.'")'."\n";
+                }
+		
+		print OUT 'lines(positions,log10(coverage))'."\n";
+		print OUT 'abline(h=log10('.$thresh.'),lwd=4,col=rgb(255,0,0,100,maxColorValue=255))'."\n";
+		print OUT 'failedpos <- positions[coverage<'.$thresh.']'."\n";
+		print OUT 'failedcov <- coverage[coverage<'.$thresh.']'."\n";
+		print OUT 'points(failedpos,log10(failedcov),col="red",pch=19)'."\n";
+		print OUT 'graphics.off()'."\n";
+		close OUT;
+		# run R script
+		system("cd $wd/Rout && Rscript exonplot.R") == 0 || die "Could not run exonplot.R with following error '$!'\n";
+		# Add to .TEX
+		print TEX '\begin{minipage}{0.5\linewidth}\centering'."\n";
+		print TEX '\includegraphics[width=\textwidth,keepaspectratio=true]{../Plots/Coverage_'.$exonstr.'.png}'."\n";
+		print TEX '\end{minipage}'."\n";
+		$col++;
+	}
+}
+## list failed exons
+if (exists($opts{'L'})) {
+    # count columns
+        my $subtitle;
+	my $head = `head -n 1 $wd/Targets.Position.Coverage`;
+	chomp($head);
+	my @cols = split(/\t/,$head);
+	my $nrcols = scalar(@cols);
+	my $covcol = $nrcols;
+	my $poscol = $nrcols -1;
+	## hash to print
+	# tex section header
+	open TEX, ">>$wd/Report/Report.tex";
+	print TEX '\subsection*{List of Failed Exons}'."\n";
+	print TEX '\underline{NOTE:} ALL exons were tested for local coverage $<$'.$thresh.' \\\\'."\n";
+	print TEX '{\footnotesize\begin{longtable}[l]{@{\extracolsep{\fill}}llll}'."\n".'\hline'."\n";
+	print TEX '\textbf{Target Name} & \textbf{Genomic Position} & \textbf{Avg.Coverage} & \textbf{Min.Coverage} \\\\'."\n".'\hline'."\n";
+	print TEX '\endhead'."\n";
+	print TEX '\hline '."\n".'\multicolumn{4}{r}{{\textsl{\footnotesize Continued on next page}}} \\\\ '."\n".'\hline' ."\n". '\endfoot' . "\n". '\endlastfoot' . "\n";
+ 
+	$col = 1;
+	open IN, "$wd/Targets.Global.Coverage";
+	while (<IN>) {
+		chomp($_);
+		my @p = split(/\t/,$_);
+		my $region = $p[0].'-'.$p[1].'-'.$p[2];
+		my $exon = $filehash{$region}{'exon'};
+		# grep exon to tmp file
+		my $exonfile = "$wd/SplitFiles/File_".$filehash{$region}{'idx'}.".txt";
+		## determine transcript orientation.
+                my $firstline = `head -n 1 $exonfile`;
+                my @firstcols = split(/\t/,$firstline);
+                my $orient = $firstcols[5];
+		my $genomicchr = $firstcols[0];
+		my $genomicstart = $firstcols[1];
+		my $genomicstop = $firstcols[2];
+
+		if ($orient eq '+') {
+			my $bps = $genomicstop - $genomicstart + 1;
+			$subtitle = "$genomicchr:".$de->format_number($genomicstart)."+".$de->format_number($genomicstop);
+
+		}
+		else {
+			my $bps = $genomicstop - $genomicstart + 1;
+			$subtitle = "$genomicchr:".$de->format_number($genomicstart)."-".$de->format_number($genomicstop);
+		}
+
+		# check if failed
+		my $cs = `cut -f $covcol '$exonfile' `;
+		my @c = split(/\n/,$cs);
+		my ($avg,$med,$min,$max,$first,$third,$ontarget) = arraystats(@c);
+
+		if ($min >= $thresh) {
+			# lowest coverage > threshold => skip
+			next;
+		}
+
+		# print to .tex table 
+		if (length($exon) > 30) {
+			$exon = substr($exon,0,27) . '...';
+		}
+		$exon =~ s/_/ /g;
+		$exon =~ s/\|/ /g;
+
+		print TEX "$exon & $subtitle & ".int($avg)." & $min ".'\\\\'."\n"; 
+	}
+	close IN;
+	print TEX '\hline'."\n";
+	print TEX '\end{longtable}}'."\n";
+	close TEX;
+}
+
+
+## Close document
+open OUT, ">>$wd/Report/Report.tex";
+print OUT '\label{endofdoc}'."\n";
+print OUT '\end{document}'."\n";
+close OUT;
+system("cd $wd/Report && tectonic Report.tex") == 0 || die "Could not run tectonic with following error '$!'\n";
+
+## mv report to output file
+system("cp -f $wd/Report/Report.pdf '$pdffile'");
+##create tar.gz file
+system("mkdir $wd/Results");
+system("cp -Rf $wd/Plots $wd/Results/");
+system("cp -Rf $wd/Report/ $wd/Results/");
+if (-e "$wd/Targets.Global.Coverage") {
+	system("cp -Rf $wd/Targets.Global.Coverage $wd/Results/");
+}
+if (-e "$wd/Targets.Position.Coverage") {
+	system("cp -Rf $wd/Targets.Position.Coverage $wd/Results/");
+}
+
+
+exit;
+
+###############
+## FUNCTIONS ##
+###############
+sub arraystats{
+	my @array = @_;
+	my $count = scalar(@array);
+	@array = sort { $a <=> $b } @array;
+	# median
+	my $median = 0;
+	if ($count % 2) { 
+		$median = $array[int($count/2)]; 
+	} else { 
+		$median = ($array[$count/2] + $array[$count/2 - 1]) / 2; 
+	} 
+	# average 
+	my $sum = 0;
+	foreach (@array) { $sum += $_; } 
+	my $average = $sum / $count;
+	# quantiles (rounded)
+	my $quart = int($count/4) ;	
+	my $first = $array[$quart];
+	my $third = $array[($quart*3)];
+	my $min = $array[0];
+	my $max = $array[($count-1)];
+	return ($average,$median,$min,$max,$first,$third,$sum);
+}
+
+sub GlobalSummary {
+	my ($bam,$targets) = @_;
+
+	my $command = "cd $wd && coverageBed -abam $bam -b $targets > $wd/Targets.Global.Coverage";
+	if (exists($commandsrun{$command})) {
+		return;
+	}
+	system($command);
+	$commandsrun{$command} = 1;
+}
+
+sub CoveragePerRegion {
+	my ($bam,$targets) = @_;
+	my $command = "cd $wd && coverageBed -abam $bam -b $targets > $wd/Targets.Global.Coverage";
+	if (exists($commandsrun{$command})) {
+		return;
+	}
+	system($command);
+	$commandsrun{$command} = 1;
+}
+
+sub SubRegionCoverage {
+	my ($bam,$targets) = @_;
+	my $command = "cd $wd && coverageBed -abam $bam -b $targets -d > $wd/Targets.Position.Coverage";
+	system($command);
+	$commandsrun{$command} = 1;
+}
+
diff -r 000000000000 -r 49788db492f7 CoverageReport.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CoverageReport.xml	Wed Oct 25 12:37:17 2017 -0400
@@ -0,0 +1,105 @@
+<tool id="CoverageReport2" name="Panel Coverage Report" version="0.0.4">
+    <description>Provide mapping statistics</description>
+    <requirements>
+      <requirement type="package" version="1.75">perl-number-format</requirement>    
+      <requirement type="package" version="3.4.1">R</requirement>
+      <requirement type="package" version="2.17.0">bedtools</requirement>
+      <requirement type="package" version="0.1.18">samtools</requirement>
+      <requirement type="package" version="0.1.6">tectonic</requirement>      
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[      
+    perl '$__tool_directory__/CoverageReport.pl'
+    ## input files
+    -b '$input1'
+    -t '$input2'
+  
+    ## output files
+    -o '$output1'
+  
+    ## run parameters
+    $perGene
+    $PositionLevel
+    -m $threshold
+    -f $frac 
+    ## sample name
+    -n '$input1.name'
+    ]]></command>
+    <inputs>
+      <param name="input1" type="data" format="bam" label="BAM file" help="BAM file of mapped reads" />
+      <param name="input2" type="data" format="bed" label="Target Regions BED" help="BED file containing regions of interest. See below for format" />
+      <param name="threshold" type="integer" value="40" label="Minimal Coverage Threshold" help="Default: 40" />   
+      <param name="frac" type="float" value="0.2" label="Fraction of Average Coverage for usage in plot" help="Default: 0.2" />
+      <param name="perGene" type="boolean" truevalue="-r" falsevalue="" checked="True" label="Plot exon coverages for all genes in targets"/>
+      <param name="PositionLevel" type="select" label="Perform Per Exon Analysis" help="Only Failed: Only those exons not reaching global coverage above threshold, or 100%. All Exons: This can take a very long time for large panels! Select all failed to check all exons for local failures." >
+	<option value='' selected="true">None</option>
+	<option value='-s'>Plot Only Globally Failed</option>
+	<option value='-S'>Plot All Failed Exons</option>
+	<option value='-A'>Plot All Exons</option>
+	<option value='-L'>List All Failed Exons</option>
+      </param>
+    </inputs>
+    <outputs>
+      <data format="pdf" name="output1" label="${tool.name} on ${on_string}: PDF Report"/>
+    </outputs>
+    <tests>
+      <test>
+	<param name="input1" value="ecoli.bam" />
+	<param name="input2" value="ecoli_6.bed" />
+	<output name="output1" value="answer.pdf" compare="sim_size"/>
+      </test>
+    </tests>
+    <help><![CDATA[
+**What it does**
+
+This tool creates a coverage report for QC purposes. By default, average coverage statistics are provided, taken from samtools flagstats. If specified, it can also create overviews per gene in the BED file, and sub-exon plots for failed exons. 
+
+------
+
+**BED format**
+
+The BED file containing targets of interest has very specific format requirements. You **must** use the following format::
+
+  Column 1: Chromosome : Use the same syntax as the references used by Galaxy. Check your sam-headers for the correct format. ('chr1' vs '1')
+  Column 2: Start Position
+  Column 3: End Position
+  Column 4: Target Name. Use : "GENE-NAME&lt;space&gt;Exon_number" : This is split on the space after 'GeneName' for correct grouping.
+  Column 5: Score : ignored, use '0'
+  Column 6: Strand: ignored,'+' or '-'
+
+.. class:: infomark 
+
+Note: The exons for the plots will be ordered in the same way as the exons in the BED file. 
+
+------
+
+**Input formats**
+
+BAM file for reads, BED file for targets.
+
+------
+
+**Outputs**
+
+The output files are a PDF report. 
+The output tables are (tab seperated txt files): 
+
+**Targets.Global.Coverage** : Original BED file + following columns::
+  - Total coverage in target
+  - Bases in target with coverage
+  - Length of target
+  - Percent of target covered
+
+**Targets.Position.Coverage** : Original BED file + following columns::
+  - Position in target region
+  - Coverage at position
+
+    ]]></help>  
+    <citations>
+      <citation type="bibtex">@ARTICLE{a1,
+      title = {This tool creates a coverage report for QC purposes.},
+      author = {Philip Mabon},
+      url = {https://github.com/galaxyproject/tools-iuc/}
+      }
+      }</citation>
+    </citations>
+</tool>
diff -r 000000000000 -r 49788db492f7 README
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README	Wed Oct 25 12:37:17 2017 -0400
@@ -0,0 +1,14 @@
+Panel Resequencing Report
+=========================
+
+Original wrapper was created by Geert Vandeweyer. It is free to use, adapt and redistribute, but  please mention the original source.
+
+Current author is Philip Mabon (Takadonet)
+
+
+History
+=======
+0.0.1 - Initial release, no dependency handling
+0.0.2 - Updated release, following toolshed recommendations.
+0.0.4 - Changing over to bioconda for samtools,bedtools,tectonic and perl modules.
+
diff -r 000000000000 -r 49788db492f7 test-data/answer.pdf
Binary file test-data/answer.pdf has changed
diff -r 000000000000 -r 49788db492f7 test-data/ecoli.bam
Binary file test-data/ecoli.bam has changed
diff -r 000000000000 -r 49788db492f7 test-data/ecoli_6.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ecoli_6.bed	Wed Oct 25 12:37:17 2017 -0400
@@ -0,0 +1,1 @@
+gi|49175990|ref|NC_000913.2|_Escherichia_coli_str._K-12_substr._MG1655,_complete_genome,_cropped_to_first_1000_nucleotides	1	1000	gi|49175990|ref|NC_000913.2|_Escherichia_coli_str._K-12_substr._MG1655,_complete_genome,_cropped_to_first_1000_nucleotides	5	6