changeset 4:f08d1b99069b draft

Deleted selected files

Binary file coVennTree/coVennTree/.DS_Store has changed

Binary file coVennTree/coVennTree/._.DS_Store has changed

--- a/coVennTree/coVennTree/coVennTree.pl	Fri Dec 12 10:24:00 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,833 +0,0 @@
-#!/usr/bin/perl
-use strict;
-use File::Basename;
-use List::MoreUtils qw( minmax );
-
-# --------------------------------------------------------------------------------------------------
-# author:	steffen lott
-# mail: 	[e-mail]
-# date: 	06-10-2014
-# version: 	1.6
-# 
-# description:
-# 	The tool converts an output from MEGAN in a special network which can visuallized with
-#	cytoscape. Gaper produces two files, the first one contains the network and the second one
-#	describes the attributes of the network. 
-# --------------------------------------------------------------------------------------------------
-
-# return version number
-if (@ARGV == 0) {
-	print "CoVennTree-Version 1.6\n";
-	print "COMMAND\n";
-	print "coventree argv0 argv1 argv2 argv3 argv4\n";
-	print "--------------\n";
-	print "argv0 = input file\n";
-	print "argv1 = color mode [1,4]\n";
-	print "argv2 = transformation function [1,7]\n";
-	print "argv3 = only leaf information => 0 ; all information => 1\n";
-	print "argv4 = output file name network\n";
-	print "argv5 = output file name attributes\n";
-	exit;
-}
-
-
-
-
-# container to represent the network
-my @network = ();
-
-
-
-# 0 PARAMETER_______________
-# read argument from command-line
-# important: DSV -> taxon-path, count(s) -> assigned -> tab
-my $megan_file = $ARGV[0];
-
-
-# 1 PARAMETER_______________
-my $colorMode;   
-# color mode for venn-diagrams 0,1,2,3,4
-if(defined $ARGV[1]){
-	$colorMode = $ARGV[1];
-}else{
-	$colorMode = 3;
-}
-
-
-# 2 PARAMETER_______________
-# 2 different transformations functions
-my $transFnc = "";
-if(defined $ARGV[2]){          # small datasets
-   	$transFnc = $ARGV[2];
-}else{
-	$transFnc = 1;
-}
-
-
-# 3 PARAMETER_______________
-# the user can switch between "only leaf information" 
-# or the complete tree information. the last one takes also the not assigned reads
-# and creates artificial nodes to keep this number
-my $onlyLeafs;
-if(defined $ARGV[3]){
-	if($ARGV[3] == 0){
-		$onlyLeafs = "on";
-	}elsif($ARGV[3] == 1){
-		$onlyLeafs = "off";
-	}
-}else{ # all information will be used! not assigned and assigned
-	$onlyLeafs     = "off";
-}
-
-# 4 PARAMETER_______________
-# output -> network
-my $out_network    = $ARGV[4];
-
-# 5 PARAMETER_______________
-# output -> attributes
-my $out_attributes = $ARGV[5];
-
-
-
-# check the input format of the file. only a file with exactly three datasets are excepted. the other one will fill up with zeros
-
-
-# read-in MEGAN-file
-# if #{data-sets} = 1 -> no heade line
-# if #{data-sets} > 1 -> heade line " #Datasets		set1	set2	..."
-open(inFile , "<$megan_file")  || die "File not found - \"Path-File\"!\n";
-my @pairIds = ();
-my $header  = "";
-my @input_file   = ();
-my @numberOfSets = ();
-
-while(<inFile>){
-	chomp($_);
-  	if($_ =~ /^#/){
-  		$header = $_;
-  		@numberOfSets = split("\t", $_);
-  	}else{
-  		#print @numberOfSets . "\n";
-  		# check the number of datasets are included
-  		if(@numberOfSets == 0 || @numberOfSets == 1 || @numberOfSets > 4){			# no set is in the file
-  			print "Error: File doesn't contain any dataset or contain more than three!";
-  			exit;
-  		}elsif(@numberOfSets == 2){		# only one set is in the file -> add 2x zeros
-  			$_ .= "\t" . 0 . "\t" . 0;
-  		}elsif(@numberOfSets == 3){		# only two sets are in the file -> add 1x zeros
-  			$_ .= "\t" . 0;
-  		}
-  		
-  		addToNetwork($_);
-  		push(@input_file, $_);
-  	}
-}
-close(inFile);
-
-
-# --------------------------------------------------------------------------------------------------------------
-# --------------------------------------------------------------------------------------------------------------
-# (1) PREPROCESSING: detect all leaf nodes
-my $modifiedInput  = detectNonLeafs();
-
-# (2) MAIN COMPUTATION: compute deep by deep (path deep ex. root;Viruses; => deep 2)
-my ($vennClusterOut, $specialNumberOut) = clusterVennBottomUp();
-
-# (3) VENN-END-PREPERATION: sum up all single values (d1-d3), transform abs values into 
-my $vennToStore    = vennForCytoscape($vennClusterOut, $specialNumberOut);
-
-# (4) SAVE RESULTS INTO FILES: one file contains the network (.sif), the other one contains the attributes
-storeNetwork();
-store2FileVenn($vennToStore);
-# --------------------------------------------------------------------------------------------------------------
-# --------------------------------------------------------------------------------------------------------------
-
-
-
-
-sub store2FileVenn{
-	my $outVenn = $_[0];
-	# test
-	my $tmpFileName = $out_attributes;
-	
-	#my $tmpFileName = "./network.venn";
-	open(FILE , ">$tmpFileName")  || die "File can't be written - \"venn - File\"!\n";
-		print FILE join("\n", @{$outVenn}) . "\n";
-	close(FILE);
-}
-
-
-sub vennForCytoscape{
-	my $vennCluster = $_[0];
-	my $specialNum  = $_[1];
-	my $specNformat = 0;
-	my @out = ();
-	# datastructure $vennCluster=> vennCluster[]{}{} => values
-	#delete $vennCluster->[0]{"no"};
-	my $frameSize = 0;
-	my $values    = 0;
-	my $googleURL = "";
-	my $outStr = "";
-	
-	for(my $i = 0 ; $i < @{$vennCluster}; $i++){
-		while ( my($key, $value) = each %{$vennCluster->[$i]} ){
-			while ( my($key2, $value2) = each %{$vennCluster->[$i]{$key}} ){
-				$values    = $vennCluster->[$i]{$key}{$key2};				
-				$frameSize = getCorrectedFrameSize($values);
-				
-				if(defined $specialNum->[$i]{$key}{$key2}){
-					$specNformat = $key2 . "[" . sprintf("%.3f", $specialNum->[$i]{$key}{$key2}) . "]";
-				}else{
-					$specNformat = $key2; 
-				}
-				
-				# old version, this version works pretty well
-				#$frameSize = getFrameSize($values);	
-				$googleURL = computeGoogleApiStrRotation($frameSize,$values,$colorMode);
-				$outStr = $key2 . "\t" . $googleURL . "\t" . $specNformat . "\t" . $values;
-				push(@out, $outStr);
-			}
-		}
-	}
-	return \@out;
-}
-
-
-# this function keep the biggest node in the lowest depth,...
-sub computeGoogleApiStrRotation{
-	my $frameSize = $_[0];
-	my $values    = $_[1];
-	my $colMode   = $_[2];
-	my @relVal    = ();
-	my @col   	  = ();
-	my %sort      = ();
-	my @store  	  = ();
-	my %ovHash    = ();
-	my @storeOldPos = ();
-	my @spVal  	  = split(" ", $values);
-	my $sum    	  = $spVal[0] + $spVal[1] + $spVal[2];	
-	
-	# user color-mode 
-	if($colMode == 0){
-		$col[0] 	  = "18A3F2";     $col[1] = "FA0800";     $col[2] = "FFF905";
-	}elsif($colMode == 1){
-		$col[0] 	  = "FF2A00";     $col[1] = "9CFF00";     $col[2] = "00CCFF";
-	}elsif($colMode == 2){
-		$col[0] 	  = "B4FF00";     $col[1] = "FF00C6";     $col[2] = "00AEFF";
-	}elsif($colMode == 3){
-		$col[0] 	  = "82FF00";     $col[1] = "7E00FF";     $col[2] = "FF003B";
-	}elsif($colMode == 4){
-		$col[0] 	  = "1A1A1A";     $col[1] = "8A8A8A";     $col[2] = "C7C7C7";
-	}
-	
-	$sort{"0"} 	  = $spVal[0]; $sort{"1"} = $spVal[1]; $sort{"2"} = $spVal[2]; 
-	
-	my $tmp = 0;
-	foreach(@spVal){
-		if($sum != 0){
-			$tmp = $_ * 100 / $sum;
-		}else{
-			$tmp = 0;
-		}
-		push(@relVal,$tmp);
-	}
-	
-	$ovHash{"01"} = $relVal[3]; $ovHash{"10"} = $relVal[3]; 
-	$ovHash{"02"} = $relVal[4]; $ovHash{"20"} = $relVal[4]; 
-	$ovHash{"21"} = $relVal[5]; $ovHash{"12"} = $relVal[5]; 
-	
-	my $url = "http://chart.apis.google.com/chart?chs=" . $frameSize . "x" . $frameSize . "&chco=";
-	# change color position in the google output string corresponding to the highest value          
-	foreach my $k( sort {$sort{$b}<=>$sort{$a}} keys %sort) {
-    	$url .= $col[$k] . ",";
-    	push(@store, $k);
-	}
-	chop($url);	    
-	          
-	$url .= "&cht=v&chd=t:";
-	# sort node values in the right order         
-	for(my $i = 0 ; $i < @relVal - 4 ; $i++){
-		#print $i . "\t" . $store[$i] . "\t" . $relVal[$store[$i]] . "\n";
-		$url .= sprintf("%.1f", $relVal[$store[$i]]) . ",";
-	}
-	# sort intersection values in the right order
-	my $tStr0 = $store[0] . $store[1];
-	my $tStr1 = $store[0] . $store[2];
-	my $tStr2 = $store[1] . $store[2];
-	$url    .= sprintf("%.1f", $ovHash{$tStr0}) . "," . sprintf("%.1f", $ovHash{$tStr1}) . "," . sprintf("%.1f", $ovHash{$tStr2}) . ",";
-	$url .= "0.0";
-	$url .= "&chf=bg,s,e0dede00";
-}
-
-
-# original function without any node rotation. the order of the nodes is always the same
-sub computeGoogleApiStr{
-	my $frameSize = $_[0];
-	my $values    = $_[1];
-	my @relVal    = ();
-	my @spVal  = split(" ", $values);
-	my $sum    = $spVal[0] + $spVal[1] + $spVal[2];	
-	
-	foreach(@spVal){
-		my $tmp = $_ * 100 / $sum;
-		push(@relVal,$tmp);
-	}
-	my $url = "http://chart.apis.google.com/chart?chs=" . $frameSize . "x" . $frameSize . 
-	          #color
-	          "&chco=FF6342,ADDE63,63C6DE" . 
-	          #"&chco=0000FF,0099FF,00FFFF" .
-	          
-	          "&cht=v&chd=t:";
-	
-	for(my $i = 0 ; $i < @relVal - 1 ; $i++){
-		$url .= sprintf("%.1f", $relVal[$i]) . ",";
-	}        
-	$url .= sprintf("%.1f", $relVal[-1]);  
-	             
-	$url .= "&chf=bg,s,e0dede00";
-}
-
-
-sub getCorrectedFrameSize{
-	my $values = $_[0];
-	my @spVal  = split(" ", $values);
-	my $sum    = $spVal[0] + $spVal[1] + $spVal[2];	
-	my $frame  = lookupPixelSQRT($sum);
-	
-	# find maxValue position ([0] - [2])
-	my $arrPos = getMaxPos($spVal[0], $spVal[1], $spVal[2]);
-	my $addOver= -1;
-	my $addNode= -1;
-	my $addSum = -1;
-	
-	if($arrPos == 0){
-		$addNode = $spVal[1] + $spVal[2];
-		$addOver = $spVal[3] + $spVal[4];
-	}elsif($arrPos == 1){
-		$addNode = $spVal[0] + $spVal[2];
-		$addOver = $spVal[3] + $spVal[5];
-	}elsif($arrPos == 2){
-		$addNode = $spVal[0] + $spVal[1];
-		$addOver = $spVal[4] + $spVal[5];
-	}
-	# if the 2 of 3 nodes have no overlap to the largest one, than the complete value
-	# will be used to compute a frame and add this to the existing frame
-	$addSum = $addNode - $addOver;
-	
-	my $addFrame = lookupPixelSQRT($addSum);
-	my $sumFrame = $frame + $addFrame;
-	return $sumFrame;
-}
-
-
-sub getMaxPos{
-	my $pos = -1;
-	if( ($_[0] >= $_[1]) && ($_[0] >= $_[2]) ){
-		$pos = 0;
-	}elsif( ($_[1] >= $_[0]) && ($_[1] >= $_[2]) ){
-		$pos = 1;
-	}else{
-		$pos = 2;
-	}
-	return $pos;
-}
-
-
-sub getFrameSize{
-	my $values = $_[0];
-	my @spVal  = split(" ", $values);
-	my $sum    = $spVal[0] + $spVal[1] + $spVal[2];	
-	my $frame  = lookupPixel($sum);
-	return $frame;
-}
-
-
-
-sub clusterVennBottomUp{
-	# transform $modifiedInput into datastructure
-	# container => [deep]{parent}{child}
-	my @container        = ();
-	my @containerSpecial = ();
-	my @nodeValues = ();
-	my $maxDeep    = 0; 
-	my %helperHash = ();
-	my %specialMatrixAll = ();
-	
-	foreach(@{$modifiedInput}){
-		my @tmpArr = split('\t', $_);
-		my @path   = split(';' , $tmpArr[0]);
-		my $deep   = @path - 1;
-		
-		if(($deep - 1) >= 0){
-			$container[$deep]{$path[-2]}{$path[-1]}  = $tmpArr[1];
-			$nodeValues[$deep]{$path[-2]}{$path[-1]} = "f";
-		}else{
-			$container[$deep]{"no"}{$path[-1]} = $tmpArr[1];
-		}
-	}
-	# start computation from the deepest path to the root node	
-	for(my $i = (@container-1) ; $i >= 0  ; $i--){
-		while ( my($key, $value) = each %{$container[$i]} ){
-			# update all predecessor nodes
-			while ( my($keyUp, $valueUp) = each %helperHash ){
-				if(exists $container[$i]{$key}{$keyUp}){
-					$container[$i]{$key}{$keyUp} = $valueUp;
-					# compute special value by decompose venn's and add special value
-					$containerSpecial[$i]{$key}{$keyUp} = vennCongruousness(\@{$specialMatrixAll{$keyUp}});
-				}
-			}
-			# group all nodes which has the same predecessor id and sum up the values	
-			while ( my($key2, $value2) = each %{$container[$i]{$key}} ){
-				if(exists $helperHash{$key}){
-					$helperHash{$key} = addValues($helperHash{$key}, $value2);
-					#push(@{$specialMatrixAll{$key}}, $value2);
-					#print $key . "\t" . $value2 . "\n";
-				}else{
-					$helperHash{$key} = $value2;
-				}
-				#print $key . "\t" . $value2 . "\n";
-				push(@{$specialMatrixAll{$key}}, $value2);
-			}			
-		}
-	}
-	return \@container, \@containerSpecial;
-}
-
-
-sub vennCongruousness{
-	my $inSpecMatrix = $_[0];
-	my $numOfSets    = @numberOfSets - 1;
-	my @arrVal  = ();  my @matrix = ();  
-	my @sum     = ();
-	my $numVenn = 0; 
-	my %actSet = ();
-	my %actOvp = ();
-	$actSet{"result"} = 0;
-	$actOvp{"result"} = 0;
-	
-	# (step 1) - sum up rows
-	foreach (@{$inSpecMatrix}){
-		@arrVal = split(" ", $_);
-		$sum[0] += $arrVal[0];    $sum[1] += $arrVal[1];     $sum[2] += $arrVal[2];
-		$sum[3] += $arrVal[3];    $sum[4] += $arrVal[4];     $sum[5] += $arrVal[5];
-		
-		if($arrVal[0] > 0){
-			if(!(exists $actSet{1})){
-				$actSet{1} = 1;
-				$actSet{"result"} += 1; 
-			}
-		}
-		if($arrVal[1] > 0){
-			if(!(exists $actSet{2})){
-				$actSet{2} = 1;
-				$actSet{"result"} += 1; 
-			}
-		}
-		if($arrVal[2] > 0){
-			if(!(exists $actSet{3})){
-				$actSet{3} = 1;
-				$actSet{"result"} += 1; 
-			}
-		}
-		if($arrVal[3] > 0){
-			if(!(exists $actOvp{1})){
-				$actOvp{1} = 1;
-				$actOvp{"result"} += 1; 
-			}
-		}
-		if($arrVal[4] > 0){
-			if(!(exists $actOvp{2})){
-				$actOvp{2} = 1;
-				$actOvp{"result"} += 1; 
-			}
-		}
-		if($arrVal[5] > 0){
-			if(!(exists $actOvp{3})){
-				$actOvp{3} = 1;
-				$actOvp{"result"} += 1; 
-			}
-		}
-	} 
-	
-	# (step 2) - calc ratios (-1)
-	my $i = 0;
-	foreach (@{$inSpecMatrix}){
-		@arrVal = split(" ", $_);
-		for(my $j = 0 ; $j < @arrVal ; $j++){ # eventuell -1 da index von 0 - 6 anstatt 0 - 5 laeuft
-			# div zero !
-			if($arrVal[$j] == 0){
-				$matrix[$i][$j] = 0;
-			}else{
-				#print $j . "\t" . $sum[$j] . " \t" . $arrVal[$j] . "\n";
-				$matrix[$i][$j] = $sum[$j] / $arrVal[$j];
-			}
-		}
-		$i++;
-	}
-	
-	$numVenn = $i;
-	# (step 3) - sum up data set ratios d1-d3 
-	@sum = (); 
-	for(my $j = 0 ; $j < @matrix; $j++){
-		$sum[0] += $matrix[$j][0];    $sum[1] += $matrix[$j][1];     $sum[2] += $matrix[$j][2];
-		$sum[3] += $matrix[$j][3];    $sum[4] += $matrix[$j][4];     $sum[5] += $matrix[$j][5];
-	}
-	# (step 4) - calc ratios -> max(d_i, #{V}) / min(d_i, #{V})
-	my @condensedM = (); my $max = 0; my $min = 0;
-	for(my $j = 0 ; $j < @sum ; $j++){
-		$max = ($numVenn, $sum[$j])[$numVenn < $sum[$j]];
-		$min = ($numVenn, $sum[$j])[$numVenn > $sum[$j]];
-		
-		if($min == 0){
-			$sum[$j] = 0;
-		}else{
-			#$sum[$j] = $max / $min;
-			$sum[$j] = $sum[$j] / $numVenn;
-		}
-		#print "-> " . $j . "\t" . $sum[$j] . "\t" . $max . "\t" . $min . "\n";
-	}
-	# (step 5) - normalize values between zero and one -> [0..1]
-	for(my $j = 0 ; $j < @sum ; $j++){
-		$max = ($numVenn, $sum[$j])[$numVenn < $sum[$j]];
-		$min = ($numVenn, $sum[$j])[$numVenn > $sum[$j]];
-		
-		if($max == 0){
-			$sum[$j] = 0;
-		}else{
-			$sum[$j] =  $min / $max;
-		}
-		#print "=> " . $j . "\t" . $sum[$j] . "\t" . $min . "\t" . $max . "\n";
-	}
-	# (step 6) - combine all decomposed values and create only one value
-	# case a: only one dataset -> $numOfSets == 1
-	if($numOfSets == 1){
-		#print "res: " . $sum[0] . "\n";
-		return $sum[0];
-	}elsif($numOfSets == 2){
-		# evtl fallunteruntescheiung
-		print "sum1: " . $sum[0] . "\t" . "sum2: " . $sum[1] . "\t" . "ovp1-2: " . $sum[3] . "\t" . "sets: " . $actSet{"result"} . "\t" . "ovp: " . $actOvp{"result"} . "\n";
-		if($actOvp{"result"} == 0){
-			my $t = ((($sum[0] + $sum[1]) / $actSet{"result"}) );
-			#print "res2 " . $t . " ***\n";
-			return ((($sum[0] + $sum[1]) / $actSet{"result"}) );
-		}else{
-			print "foobar\n";
-			my $t = ((((($sum[0] + $sum[1]) / $actSet{"result"}) + $sum[3]) / 2) );
-			#print "res2* " . $t . " ***\n";
-			return ((((($sum[0] + $sum[1]) / $actSet{"result"}) + $sum[3]) / 2) );
-		}
-	}elsif($numOfSets == 3){
-		#print $sum[0] . "\t" . $sum[1] . "\t" . $sum[2] . "\t" . $sum[3] . "\t" . $sum[4] . "\t" . $sum[5] . "\n";
-		#print $actSet{"result"} . "\t" . $actOvp{"result"} . "\n";
-		#return ((((($sum[0] + $sum[1] + $sum[2]) / $numOfSets) + (($sum[3] + $sum[4] + $sum[5]) / $numOfSets) ) / 2) );
-		
-		if($actOvp{"result"} == 0){
-			my $t = (($sum[0] + $sum[1] + $sum[2]) / $actSet{"result"});
-			#print ">>>>>>> " . $t. "\n";
-			return (($sum[0] + $sum[1] + $sum[2]) / $actSet{"result"});
-		}else{
-			my $t = ((((($sum[0] + $sum[1] + $sum[2]) / $actSet{"result"}) + (($sum[3] + $sum[4] + $sum[5]) / $actOvp{"result"}) ) / 2));
-			#print ">>>>>>> " . $t. "\n";
-			return ((((($sum[0] + $sum[1] + $sum[2]) / $actSet{"result"}) + (($sum[3] + $sum[4] + $sum[5]) / $actOvp{"result"}) ) / 2));
-		}
-	}else{
-		return -1;
-	}
-}
-
-
-# save version of function clusterVennBottomUp()
-#sub clusterVennBottomUp{
-#	# transform $modifiedInput into datastructure
-#	# container => [deep]{parent}{child}
-#	my @container  = ();
-#	my $maxDeep    = 0; 
-#	my %helperHash = ();
-#	
-#	foreach(@{$modifiedInput}){
-#		my @tmpArr = split('\t', $_);
-#		my @path   = split(';' , $tmpArr[0]);
-#		my $deep   = @path - 1;
-#		
-#		if(($deep - 1) >= 0){
-#			$container[$deep]{$path[-2]}{$path[-1]} = $tmpArr[1];
-#		}else{
-#			$container[$deep]{"no"}{$path[-1]} = $tmpArr[1];
-#		}
-#	}
-#	# start computation from the deepest path to the root node	
-#	for(my $i = (@container-1) ; $i >= 0  ; $i--){
-#		while ( my($key, $value) = each %{$container[$i]} ){
-#			# update all predecessor nodes
-#			while ( my($keyUp, $valueUp) = each %helperHash ){
-#				if(exists $container[$i]{$key}{$keyUp}){
-#					$container[$i]{$key}{$keyUp} = $valueUp;
-#				}
-#			}
-#			# group all nodes which has the same predecessor id and sum up the values	
-#			while ( my($key2, $value2) = each %{$container[$i]{$key}} ){		
-#				if(exists $helperHash{$key}){
-#					$helperHash{$key} = addValues($helperHash{$key}, $value2);
-#				}else{
-#					$helperHash{$key} = $value2;
-#				}
-#			}
-#		}
-#	}
-#	return \@container;
-#}
-
-
-
-sub addValues{
-	my $val1 = $_[0];
-	my $val2 = $_[1];
-	
-	my @sV1 = split(" ", $val1);
-	my @sV2 = split(" ", $val2);
-
-	my $tmp = $sV1[0] + $sV2[0];
-	my $out = $tmp;
-	
-	for(my $i = 1 ; $i < @sV1 ; $i++){
-		$tmp = $sV1[$i] + $sV2[$i];
-		$out .= " " . $tmp;
-	}
-	return $out;
-}
-
-
-
-# detect non leaf nodes and remove the values
-# works on @input_file !!!
-# this version works only with 3 depths!
-sub detectNonLeafs{
-	my %recursiveValues = ();
-	my @modifiedFile    = ();
-	my $convertedPath   = "";
-	
-	my @additionalNetwork = ();
-	
-	# read last line
-	my @tmpArr1 = split('\t',$input_file[($#input_file)],2);
-	# -2 path direction from reward instead from the beginning. (-1 leaf,child , -2 parent,inner node)
-	my $parent1 = getId($tmpArr1[0],-2);
-	my $child1  = getId($tmpArr1[0],-1); 
-	my $deep1   = getPathDeep($tmpArr1[0]);
-	my $parent2 = "";
-	my $child2  = "";  
-	my $deep2   = 0;
-	
-	
-	# if "if-statement is true, only root node exists"
-	my $outStr = "";
-	if($parent1 == -1){
-		$outStr = convertPath($tmpArr1[0]) . "\t" . computeLeafValues($tmpArr1[1]);
-		push(@modifiedFile, $outStr);
-	}else{
-		$outStr = convertPath($tmpArr1[0]) . "\t" . computeLeafValues($tmpArr1[1]);
-		push(@modifiedFile, $outStr);
-	
-		for(my $i = (@input_file-2) ; $i >= 0 ; $i--){
-			@tmpArr1 = split('\t',$input_file[$i],2);
-			$parent2 = getId($tmpArr1[0],-2);
-			$child2  = getId($tmpArr1[0],-1); 
-			$deep2   = getPathDeep($tmpArr1[0]);
-			
-			#print $parent2 . "\t" . $child2 . "\n";
-			
-			# if eq true -> new leaf
-			if($parent2 eq $parent1){
-				$outStr = convertPath($tmpArr1[0]) . "\t" . computeLeafValues($tmpArr1[1]);
-				push(@modifiedFile, $outStr);
-			}elsif($parent1 eq $child2){
-				$outStr = convertPath($tmpArr1[0]) . "\t" . "undef";
-				push(@modifiedFile, $outStr);
-				
-				my @check = split('\t', $tmpArr1[1]);
-				my $tSum  = 0;
-				foreach(@check){
-					$tSum += $_;
-				}
-				if(($onlyLeafs eq "off") && ($tSum > 0)){
-					$outStr = convertPath($tmpArr1[0]) . "not_assigned_" . $child2 . ";" . "\t" . computeLeafValues($tmpArr1[1]);
-					push(@modifiedFile, $outStr);
-					$outStr = $child2 . " pp " . "not_assigned_" . $child2;
-					push(@network, $outStr);
-				}
-			}else{
-				$outStr = convertPath($tmpArr1[0]) . "\t" . computeLeafValues($tmpArr1[1]);
-				push(@modifiedFile, $outStr);
-			}			
-			
-			if($parent1 == -1){
-				push(@modifiedFile, convertPath($tmpArr1[0]));
-				last;	
-			}
-			$parent1 = $parent2;
-			$child1  = $child2;
-			$deep1   = $deep2;
-		}
-	}
-	# store @additionalNetwork in .sif file!!! at this point, the sif file exists!
-	# it is stored into @network container. this container is globel defined!
-	
-	return \@modifiedFile;
-}
-
-
-# helper function for detectNonLeafs 
-sub getPathDeep{
-	my $inPath = $_[0];
-	my @deep = split(';', $inPath);
-	my $size = $#deep;
-	return $size;
-}
-
-sub convertPath{
-	my $inString = $_[0];
-	$inString =~ s/"//g;
-	$inString =~ s/\s+/_/g;
-	return $inString;
-}
-
-sub getId{
-	my $lineToParse = $_[0];
-	my $idPos       = $_[1];
-	my $stringId = "";
-	my @path     = ();
-	
-	$lineToParse =~ s/"//g;
-	$lineToParse =~ s/\s+/_/g;
-	@path = split(';',$lineToParse);
-	my $num = @path;
-	
-	if(($num + $idPos) < 0){
-		return -1;
-	}else{
-		return $path[$idPos];	
-	}
-}
-
-sub computeLeafValues{
-	my $meganValues = $_[0];
-	my @rawValues   = split('\t', $meganValues);
-	my @nodeRelVal  = ();
-	
-	my $outValues   = $rawValues[0] . " " . $rawValues[1] . " " . $rawValues[2]; 
-
-	if($rawValues[0] <= $rawValues[1]){
-		$outValues .= " " . $rawValues[0];
-	}else{
-		$outValues .= " " . $rawValues[1];
-	}
-	if($rawValues[0] <= $rawValues[2]){
-		$outValues .= " " . $rawValues[0];
-	}else{
-		$outValues .= " " . $rawValues[2];
-	}
-	if($rawValues[1] <= $rawValues[2]){
-		$outValues .= " " . $rawValues[1];
-	}else{
-		$outValues .= " " . $rawValues[2];
-	}
-	#my ($min, $max) = minmax @rawValues;
-	my $min = 0;
-	$outValues .= " " . $min;
-	
-	return $outValues;
-}
-# -----------------------------------------------------------------------------
-
-
-# compute network (.sif)
-sub addToNetwork{
-	my $inLine = $_[0];
-	my @splitInLine = split('\t',$inLine);
-	# remove ' " ' from line
-	$splitInLine[0] =~ s/"//g;
-	$splitInLine[0] =~ s/\s+/_/g;
-	my @elements    = split(';' ,$splitInLine[0]); 
-		
-	if(@elements > 1){
-		my $outString = $elements[-2] . " pp " . $elements[-1];
-		push(@network, $outString);
-	}
-}
-
-
-# store network in .sif file
-sub storeNetwork{
-	# test
-	my $tmpFileName = $out_network;
-	
-	#my $tmpFileName = "./network.sif";
-	open(FILE , ">$tmpFileName")  || die "File can't be written - \"sif - File\"!\n";
-		print FILE join("\n", @network) . "\n";
-	close(FILE);
-}
-
-
-# ---------------------------------------------------------------------------------------------
-# two different lookup-tables are available!
-# lookupPixel() => static ; lookupPixelSQRT() => dynamic
-#
-# lookup absolute node-size to pixel (frame-size for venn-diagram)
-sub lookupPixel{
-	my $query = $_[0];
-	
-	if($query < 10){
-		return 30;
-	}elsif($query < 100){
-		return 40;
-	}elsif($query < 1000){
-		return 50;
-	}elsif($query < 10000){
-		return 60;
-	}elsif($query < 100000){
-		return 80;
-	}elsif($query < 1000000){
-		return 100;
-	}elsif($query < 10000000){
-		return 140;
-	}elsif($query < 20000000){
-		return 180;
-	}elsif($query < 30000000){
-		return 220;
-	}else{
-		return 250;	
-	}
-}
-
-# lookup absolute node-size to pixel (frame-size for venn-diagram) <- this is currently used!
-sub lookupPixelSQRT{
-	
-	if ($transFnc == 0) {
-		return int(($_[0] ** (1/(1.6))) * 1.8 + 8);  # 3,000 datapoints in sum
-	}elsif($transFnc == 1){
-		return int(($_[0] ** (1/(2.1))) * 1.8 + 8);  # 30,000 datapoints in sum
-	}elsif($transFnc == 2){
-		return int(($_[0] ** (1/(2.6))) * 1.8 + 8);  # 300,000 datapoints in sum
-	}elsif($transFnc == 3){
-		return int(($_[0] ** (1/(3.1))) * 1.8 + 8);  # 3,000,000 datapoints in sum
-	}elsif($transFnc == 4){
-		return int(($_[0] ** (1/(3.7))) * 1.8 + 8);  # 30,000,000 datapoints in sum
-	}elsif($transFnc == 5){
-		return int(($_[0] ** (1/(4))) * 1.8 + 8);    # 300,000,000 datapoints in sum
-	}elsif($transFnc == 6){
-		return int(($_[0] ** (1/(4.7))) * 1.8 + 8);  # 3,000,000,000 datapoints in sum
-	}
-	
-	#return int(($_[0] ** (1/(3.3))) * 1.8 + 30);	# test version for small and large datasets?
-	#return int(($_[0] ** (1/(3.3))) * 1.8 + 5);	# test version for small and large datasets?
-	#return int(($_[0] ** (1/(4))) * 1.8 + 8);	    # test version for small and large datasets?
-	#return int(($_[0] ** (1/6)) * 12);				# old version this version is good for large datasets
-}
-
-
-
-
-
-
-
-

--- a/coVennTree/coVennTree/coVennTree.xml	Fri Dec 12 10:24:00 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,143 +0,0 @@
-<tool id="coVennTree" name="CoVennTree (Comparative weighted Venn Tree) - Rooted Tree" version="1.6.0">
-    <description>Comparative rooted tree analysis for files in dsv format</description>
-    <requirements>
-        <requirement type="package" version="1.6">coVennTree</requirement>
-        <requirement type="package" version="5.18.1">perl</requirement>
-    </requirements>
-    <command interpreter="perl">
-        coVennTree.pl
-        $infile
-        $color_mode
-        $trans_func
-        $leafs_allInformation
-        $outfile_network
-        $outfile_attribute
-    </command>
-    
-    <inputs>
-        <param name="infile" type="data" format="tabular" label="Path File" help="Tabular file containing the paths and values"/>
-        
-      
-        <param name="color_mode" multiple="false" type="select" label="Select color mode for Venn diagrams">
-                <option value="0">(1) Set1: blue       Set2: red       Set3: yellow</option>
-                <option value="1">(2) Set1: red        Set2: green     Set3: blue</option>
-                <option value="2">(3) Set1: green      Set2: magenta   Set3: blue</option>
-                <option value="3">(4) Set1: green      Set2: purple    Set3: red</option>
-                <option value="4">(5) Set1: dark gray  Set2: mid-grey  Set3: light gray</option>
-        </param>
-        
-             
-        <param name="trans_func" multiple="false" type="select" label="Select transformation function">
-                <option value="0">(1) datasets max: 3,000 data points in sum</option>
-                <option value="1">(2) datasets max: 30,000 data points in sum</option>
-                <option value="2">(3) datasets max: 300,000 data points in sum</option>
-                <option value="3">(4) datasets max: 3,000,000 data points in sum</option>
-                <option value="4">(5) datasets max: 30,000,000 data points in sum</option>
-                <option value="5">(6) datasets max: 300,000,000 data points in sum</option>
-                <option value="6">(7) datasets max: 3,000,000,000 data points in sum</option>
-        </param>
-       
-        
-        <param name="leafs_allInformation" multiple="false" type="select" label="Select tree analyzes function">
-                <option value="1">(1) leaf + inner nodes informations</option>
-                <option value="0">(2) only leaf information</option>
-        </param>
-        
-    </inputs>
-    
-    <outputs>
-        <data format="tabular" name="outfile_network" label="Network" />
-        <data format="tabular" name="outfile_attribute" label="Attributes" />
-    </outputs>
-    
-    <tests>
-        <test>
-        </test>
-    </tests>
-    
-    <help>
-.. class:: infomark
-
-CoVennTree compares up to three rooted trees at the same time.
-
-CoVennTree (Comparative weighted Venn Tree) is a software to analyze and compare up to three datasets. Unlike other
-methods, CoVennTree correlates data on the leaf level and transfers this information to the root node. CoVennTree works with numbers to compute weighted
-Venn diagrams for each node in the graph (rooted tree). Therefore any kind of input data can be processed as long as the data structure will be taken into account.
-
-
-
-**Input**
-
-*Input example*
-
-
-.. image:: $PATH_TO_IMAGES/example1.png 
-  :height: 430 
-  :width: 600
-
-
-*dsv-format: The following table represents the graph.*
-
-
-===========  ======  ======  ======
-#Datasets    set1    set2    set3
-===========  ======  ======  ======
-"root;"      0       0       0
-"root;A;"    10000   0       0
-"root;A;C;"  600000  300000  500000
-"root;A;D;"  0       100000  200000
-"root;A;E;"  800000  0       100000
-"root;B;"    10000   20000   50000
-===========  ======  ======  ======
-
-
--------
-
-
-**Results**
-
-A specific color is assigned to each dataset in five optional color schemes (see parameter "Select color mode for weighted Venn diagrams").
-In this example set1 corresponds to color blue, set2 to red and set3 to yellow.
-In order to cover a wide numerical range a non linear transformation function is used.
-
-
-*Data format \*.sif*
-
-[parent_node]   [connected_with]    [child_node]
-
-
-*Data format \*.venn*
-
-[id]    [google_url]    [id_vds]    [Venn_abs_values]
-
-
-*Output example "leaf information and not assigned information"*
-
-By selecting "leaf information + not assigned information" artificial nodes can be inserted.
-Artificial nodes will be inserted if inner nodes have values larger than zero.
-
-.. image:: $PATH_TO_IMAGES/venn-graph-off.png 
-  :height: 358 
-  :width: 425
-  
-  
--------
-
-
-*Output example "only leaf information"*
-
-By selecting "only leaf information" only leaf nodes are considered for the computation of weighted Venn diagrams.
-
-.. image:: $PATH_TO_IMAGES/venn-graph-on.png 
-  :height: 358
-  :width: 400
-
-
-
-    </help>
-    <citations>
-        <citation type="doi">
-        
-        </citation>>
-    </citations>
-</tool>

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--- a/coVennTree/coVennTree/tool_dependencies.xml	Fri Dec 12 10:24:00 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,21 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <package name="perl" version="5.18.1">
-        <repository changeset_revision="a1a111b9faa5" name="package_perl_5_18" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="coVennTree" version="1.6">
-        <install version="1.0">
-            <actions>
-                <action type="setup_perl_environment">
-                    <repository changeset_revision="a1a111b9faa5" name="package_perl_5_18" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
-                        <package name="perl" version="5.18.1" />
-                    </repository>
-                   <!-- allow downloading and installing an Perl package from cpan.org-->
-                   <package>http://search.cpan.org/CPAN/authors/id/A/AD/ADAMK/List-MoreUtils-0.33.tar.gz</package>
-                </action>
-            </actions>
-        </install>
-        <readme>
-        </readme>
-    </package>
-</tool_dependency>