# HG changeset patch
# User mcharles
# Date 1402914085 14400
# Node ID 1bf299f77ce64cc43e7cb8800eaad62b11f7e303
# Parent  26d2c851d48e118054334e82534fbd22ee28607d
Uploaded

diff -r 26d2c851d48e -r 1bf299f77ce6 filtersamunique/filtersamunique.pl
--- a/filtersamunique/filtersamunique.pl	Mon Jun 16 06:18:07 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,20 +0,0 @@
-#!/usr/bin/perl
-use strict;
-use warnings;
-
-open(IN, $ARGV[0]) or die ("Can't open $ARGV[0]\n");
-while (my $line=<IN>){
-	if ($line =~ /^\@/){
-		#Header conservation
-		print $line;
-	}
-	else {
-		#Optionnal flag verification
-		if (($line =~ /XT\:A\:U/)&&($line =~ /X0\:i\:1/)&&($line =~ /X1\:i\:0\s/)){
-			print $line;
-		}
-	}
-}
-
-
-close (IN);
\ No newline at end of file
diff -r 26d2c851d48e -r 1bf299f77ce6 filtersamunique/filtersamunique.xml
--- a/filtersamunique/filtersamunique.xml	Mon Jun 16 06:18:07 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,18 +0,0 @@
-<tool id="filtersamunique" name="filtersamunique" version="0.01">
-<description>Filter SAM file for uniquelly match reads</description>
-<command interpreter="perl">
-    filtersamunique.pl $input_sam_file > $output_file 
-</command>
-<inputs>
-<param name="input_sam_file"  type="data" format="sam" label="Select a suitable input SAM file from your history"/>
-</inputs>
-<outputs>
- <data name="output_file" format="sam" label="${tool.name} on ${on_string}"/>
-</outputs>
-
-<help>
-
-
-
-</help>
-</tool>
diff -r 26d2c851d48e -r 1bf299f77ce6 listfiltering/listfiltering.pl
--- a/listfiltering/listfiltering.pl	Mon Jun 16 06:18:07 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,61 +0,0 @@
-#!/usr/bin/perl
-use strict;
-use Getopt::Long;
-
-my $inputfile;
-my $headerfile;
-my $nb_col=1;
-my %header;
-
-if ($#ARGV<0){
-	print "\n";
-	print "perl 021_ListFiltering.pl -input_file <file> -header_file <file> -nb_col <integer>[1]\n";
-	exit(0);
-}
-
-GetOptions (
-"input_file=s" => \$inputfile,
-"header_file=s" => \$headerfile,
-"nb_col=i" => \$nb_col
-) or die("Error in command line arguments\n");
-
-open(HF, $headerfile)  or die("Can't open $headerfile\n");
-while (my $line=<HF>){
-	chomp($line);
-	my @fields = split(/\s+/,$line);
-	my $ref="";
-	my $compt=0;
-	while ($compt<$nb_col){
-		if ($ref){$ref.="\t";}
-		$ref.=$fields[$compt];
-		$compt++;
-	}
-	# my $ref = "$fields[0]\t$fields[1]";
-	$header{$ref}=$line;
-}
-close (HF);
-
-
-open(IF, $inputfile)  or die("Can't open $inputfile\n");
-while (my $line=<IF>){
-	my @fields = split(/\s+/,$line);
-	my $ref="";
-	my $compt=0;
-	while ($compt<$nb_col){
-		if ($ref){$ref.="\t";}
-		$ref.=$fields[$compt];
-		$compt++;
-	}
-	# my $ref = "$fields[0]\t$fields[1]";
-
-	if ($header{$ref}){
-		# print $line;
-		# print $header{$ref},"\n";
-	}
-	else {
-		print $line;
-	}
-	
-}
-close(IF);
-
diff -r 26d2c851d48e -r 1bf299f77ce6 listfiltering/listfiltering.xml
--- a/listfiltering/listfiltering.xml	Mon Jun 16 06:18:07 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,20 +0,0 @@
-<tool id="listfiltering" name="listfiltering" version="0.01">
-<description>Compare listA and listB first X column and remove from listA the elements present in listB</description>
-<command interpreter="perl">
-    listfiltering.pl -input_file $input_listA -header_file $input_listB -nb_col $nb_col > $output_file 
-</command>
-<inputs>
-<param name="input_listA"  type="data" format="pileup" label="Select a suitable input file from your history"/>
-<param name="input_listB"  type="data" format="txt" label="Select a suitable input file from your history"/>
-<param name="nb_col" type="integer" value="2" label="Number of column to compare"/>
-</inputs>
-<outputs>
- <data name="output_file" format="pileup" label="${tool.name} on ${on_string}"/>
-</outputs>
-
-<help>
-
-
-
-</help>
-</tool>
diff -r 26d2c851d48e -r 1bf299f77ce6 mpileupfilter/mpileupfilter.pl
--- a/mpileupfilter/mpileupfilter.pl	Mon Jun 16 06:18:07 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,394 +0,0 @@
-#!/usr/bin/perl
-use strict;
-use Getopt::Long;
-
-#
-# Filter a pileup file on forward/reverse presence and %read having the variant
-# The error code 
-#  1 : multiple variant type detected insertion/deletion/mutation
-#  1i : inconsistency in insertion
-#  1d : inconsistency in deletion
-#  1m : inconsistency in mutation
-#  2 : insufficient depth	
-#  3 : insufficient variant frequency 
-#  4 : variant position not covered by forward and reverse reads
-#  5 : variant with other variant in neighbourhood
-#  6 : too much depth
-#  8 : parsing error (couldn't parse the mpileup line correctly)
-#  9 : parsing error (couldn't parse the readbase string correctly)
-
-
-my $inputfile;
-my $logfile;
-my $MIN_DISTANCE=0;
-my $MIN_VARIANTFREQUENCY=0;
-my $MIN_FORWARDREVERSE=0;
-my $MIN_DEPTH=0;
-my $MAX_DEPTH=500;
-my $VERBOSE=0;
-my $ONLY_UNFILTERED_VARIANT="OFF";
-
-if ($#ARGV<0){
-	print "\n";
-	print "perl 020_FilterPileupv6 -input_file <mpileup_file> [OPTION]\n";
-	print "-input_file \tinputfile in mpileup format\n";
-	print "-log_file \tlogfile containing discarded mpileup lines and the errorcode associated\n";
-	print "-min_depth \tminimum depth required [1]\n";
-	print "-max_depth \tmaximim depth (position with more coverage will be discarded) [100]\n";
-	print "-min_frequency \tminimum variant frequency (0->1) [1] (default 1 => 100% reads show the variant at this position)\n";
-	print "-min_distance \tminimum distance between variant [0]\n";
-	print "-min_forward_and_reverse \tminimum number of reads in forward and reverse covering the variant required [0]\n";
-	print "\n";
-	exit(0);
-}
-
-GetOptions (
-"input_file=s" => \$inputfile,
-"log_file=s" => \$logfile,
-"min_depth=i" => \$MIN_DEPTH,
-"max_depth=i" => \$MAX_DEPTH,
-"min_frequency=f" => \$MIN_VARIANTFREQUENCY,
-"min_distance=i" => \$MIN_DISTANCE,
-"min_forward_and_reverse=i" => \$MIN_FORWARDREVERSE,
-"variant_only=s" => \$ONLY_UNFILTERED_VARIANT,
-"v=i" => \$VERBOSE
-) or die("Error in command line arguments\n");
-
-
-open(IF, $inputfile)  or die("Can't open $inputfile\n");
-
-my @tbl_line;
-my @tbl_variant_position;
-my @tbl_variant_chr;
-my @tbl_variant_refbase;
-my @tbl_variant_coverage;
-my @tbl_variant_readbase_string;
-my @tbl_variant_quality_string;
-
-#Extraction des variants
-my $nb_line=0;
-while (my $line=<IF>){
-	$nb_line++;
-	if (($nb_line % 1000000 == 0)&&($VERBOSE==1)){
-		print "$nb_line\n";
-	}
-	my $error_code=0;
-	if ($line=~/(.*?)\s+(\d+)\s+([ATGCN])\s+(\d+)\s+(.*?)\s+(.*?)$/){
-		my $current_chromosome = $1;
-		my $current_position = $2;
-		my $current_refbase = $3;
-		my $current_coverage = $4;
-		my $current_readbase_string = $5;
-		my $current_quality_string = $6;
-		
-		#Suppression of mPileUp special character
-		$current_readbase_string =~ s/\$//g; #the read start at this position
-		$current_readbase_string =~ s/\^.//g; #the read end at this position followed by quality char
-		
-		if ($current_readbase_string =~ /[ATGCNatgcn\d]/){
-			push(@tbl_line,$line);
-			push(@tbl_variant_chr,$current_chromosome);
-			push(@tbl_variant_position,$current_position);
-			push(@tbl_variant_refbase,$current_refbase);
-			push(@tbl_variant_coverage,$current_coverage);
-			push(@tbl_variant_readbase_string,$current_readbase_string);
-			push(@tbl_variant_quality_string,$current_quality_string);
-			if ($ONLY_UNFILTERED_VARIANT eq "ON"){
-				print $line;
-			}
-			
-		}
-		else {
-			#Position with no variant
-		}
-		
-	}
-	else {
-		#Error Parsing
-		print STDERR "$line #8";
-	}
-}
-close(IF);
-
-if ($ONLY_UNFILTERED_VARIANT eq "ON"){
-	exit(0);
-}
-
-####Checking the distance between variant and other filter
-
-if ($logfile){
-	open(LF,">$logfile") or die ("Cant't open $logfile\n");
-}
-
-for (my $i=0;$i<=$#tbl_line;$i++){
-	# print "ligne : $tbl_line[$i]\n";
-				
-	my $error_code=0;
-	if ($i==0){
-		#Comparing $i and $i+1 for neighbourhood filter;
-		if ($#tbl_line>0){
-			if (($tbl_variant_chr[$i+1] eq $tbl_variant_chr[$i])&&($tbl_variant_position[$i]+$MIN_DISTANCE>=$tbl_variant_position[$i+1])){
-				$error_code=5;
-				chomp($tbl_line[$i]);
-				if ($logfile){
-					print LF "$tbl_line[$i]\tcode:$error_code\n";
-				}
-				next;
-			}
-		}
-
-		#Additionnal filters
-		$error_code = check_error($tbl_variant_chr[$i],$tbl_variant_position[$i],$tbl_variant_refbase[$i],$tbl_variant_coverage[$i],$tbl_variant_readbase_string[$i]);
-
-	}
-	else {
-		#Compairing $i and $i-1 for neighbourhood filter
-		if (($tbl_variant_chr[$i-1] eq $tbl_variant_chr[$i])&&($tbl_variant_position[$i-1]+$MIN_DISTANCE>=$tbl_variant_position[$i])){
-			$error_code=5;
-			chomp($tbl_line[$i]);
-			if ($logfile){
-				print LF "$tbl_line[$i]\tcode:$error_code\n";
-			}
-			next;
-		}
-		else {
-			#Additionnal filters
-			$error_code = check_error($tbl_variant_chr[$i],$tbl_variant_position[$i],$tbl_variant_refbase[$i],$tbl_variant_coverage[$i],$tbl_variant_readbase_string[$i]);
-		}
-	}
-	if ($error_code == 0){
-		print $tbl_line[$i];
-	}
-	else {
-		chomp($tbl_line[$i]);
-		if ($logfile){
-			print LF "$tbl_line[$i]\tcode:$error_code\n";
-		}
-	}
-}
-
-if ($logfile){
-	close (LF);
-}
-
-sub check_error{
-	my $current_chromosome = shift;
-	my $current_position = shift;
-	my $current_refbase = shift;
-	my $current_coverage = shift;
-	my $current_readbase_string = shift;
-	
-	# print "test : $current_readbase_string\n";
-	
-
-	
-	#Extraction of insertions
-	
-	##################################################################
-	# my @IN = $current_readbase_string =~ m/\+[0-9]+[ACGTNacgtn]+/g;
-	# my @DEL = $current_readbase_string =~ m/\-[0-9]+[ACGTNacgtn]+/g;
-	# print "IN : @IN\n";
-	# print "DEL :@DEL\n";
-	#$current_readbase_string=~s/[\+\-][0-9]+[ACGTNacgtn]+//g; 
-	##################################################################
-	#!!! marche pas : exemple .+1Ct. correspond a . / +1C / t /. mais le match de l'expression vire +1Ct
-	##################################################################
-	
-	# => parcours de boucle
-	my @readbase = split(//,$current_readbase_string);
-	my $cleaned_readbase_string="";
-	my @IN;
-	my @DEL;
-	my $current_IN="";
-	my $current_DEL="";
-	my $current_size=0;
-	
-	for (my $i=0;$i<=$#readbase;$i++){
-		if ($readbase[$i] eq "+"){
-			#Ouverture de IN
-			$current_IN="+";
-			
-			#Recuperation de la taille
-			my $sub = substr $current_readbase_string,$i;
-			if ($sub=~/^\+(\d+)/){
-				$current_size = $1;
-			}
-			my $remaining_size = $current_size;
-			while (($remaining_size>0)&&($i<=$#readbase)){
-				$i++;
-				$current_IN.=$readbase[$i];
-				if ($readbase[$i]=~ /[ATGCNatgcn]/){
-					$remaining_size--;
-				}
-			}
-			push(@IN,$current_IN);
-		}
-		elsif ($readbase[$i] eq "-"){
-			#Ouverture de DEL
-			$current_DEL="-";
-			
-			#Recuperation de la taille
-			my $sub = substr $current_readbase_string,$i;
-			if ($sub=~/^\-(\d+)/){
-				$current_size = $1;
-			}
-			my $remaining_size = $current_size;
-			while (($remaining_size>0)&&($i<=$#readbase)){
-				$i++;
-				$current_DEL.=$readbase[$i];
-				if ($readbase[$i]=~ /[ATGCNatgcn]/){
-					$remaining_size--;
-				}
-			}
-			push(@DEL,$current_DEL);
-			
-		}
-		else {
-			#Ajout a la string
-			$cleaned_readbase_string .= $readbase[$i];
-		}
-	}
-
-	
-	# print "IN : @IN\n";
-	# print "DEL :@DEL\n";
-	# print "$cleaned_readbase_string\n";	
-	
-	my @current_readbase_array = split(//,$cleaned_readbase_string);
-
-	#Filtering : error detection
-
-	if ($#current_readbase_array+1 != $current_coverage){
-		return 9;
-		#parsing error (couldn't parse the readbase string correctly)
-	}
-	elsif ($current_coverage<$MIN_DEPTH){
-		return 2;
-		#  2 : insufficient depth
-	}
-	elsif ($current_coverage>$MAX_DEPTH){
-		return 6;
-		#  6 : too much depth
-	}
-	else {
-		if ($#IN>=0){
-			if (($cleaned_readbase_string=~/[ACGTNacgtn]/)){
-				return 1;
-				#  1 : variant type overload (multiple variant type detected insertion/deletion/mutation)
-			}
-			else {
-				########## TEST de coherence des insertions ################
-				# for (my $i=0;$i<=$#IN;$i++){
-					# if (uc($IN[0]) ne uc($IN[$i])){
-						# print uc($IN[0]),"\n";
-						# print uc($IN[$i]),"\n";
-						# return "1i";
-					# }
-				# }		
-				###########################################################
-
-				if($#IN+1 < $current_coverage*$MIN_VARIANTFREQUENCY){
-					return 3;
-					#  3 : insufficient variant frequency 
-				}
-			}
-		}
-		elsif ($#DEL>=0){
-			if (($cleaned_readbase_string=~/[ACGTNacgtn]/)){
-				return 1;
-				#  1 : variant type overload (multiple variant type detected insertion/deletion/mutation)
-			}
-			else {
-				########## TEST de coherence des deletions ################
-				# for (my $i=0;$i<=$#DEL;$i++){
-					# if (uc($DEL[0]) ne uc($DEL[$i])){
-						# print uc($DEL[0]),"\n";
-						# print uc($DEL[$i]),"\n";
-						# return "1d";
-					# }
-				# }
-				###########################################################
-
-				if($#DEL+1 < $current_coverage*$MIN_VARIANTFREQUENCY){
-					return 3;
-					#  3 : insufficient variant frequency 
-				}
-			}
-		}
-		else {
-			my $nbA=0;
-			$nbA++ while ($current_readbase_string =~ m/A/g);
-			my $nbC=0;
-			$nbC++ while ($current_readbase_string =~ m/C/g);
-			my $nbT=0;
-			$nbT++ while ($current_readbase_string =~ m/T/g);
-			my $nbG=0;
-			$nbG++ while ($current_readbase_string =~ m/G/g);
-			my $nbN=0;
-			$nbN++ while ($current_readbase_string =~ m/N/g);
-			my $nba=0;
-			$nba++ while ($current_readbase_string =~ m/a/g);
-			my $nbc=0;
-			$nbc++ while ($current_readbase_string =~ m/c/g);
-			my $nbt=0;
-			$nbt++ while ($current_readbase_string =~ m/t/g);
-			my $nbg=0;
-			$nbg++ while ($current_readbase_string =~ m/g/g);
-			my $nbn=0;
-			$nbn++ while ($current_readbase_string =~ m/n/g);
-
-			if (($nbA+$nba>0)&&($nbT+$nbt+$nbG+$nbg+$nbC+$nbc+$nbN+$nbn>0)){
-				return "1m";
-			}
-			if (($nbT+$nbt>0)&&($nbA+$nba+$nbG+$nbg+$nbC+$nbc+$nbN+$nbn>0)){
-				return "1m";
-			}
-			if (($nbG+$nbg>0)&&($nbA+$nba+$nbT+$nbt+$nbC+$nbc+$nbN+$nbn>0)){
-				return "1m";
-			}
-			if (($nbC+$nbc>0)&&($nbA+$nba+$nbT+$nbt+$nbG+$nbg+$nbN+$nbn>0)){
-				return "1m";
-			}
-			if (($nbN+$nbn>0)&&($nbA+$nba+$nbT+$nbt+$nbG+$nbg+$nbC+$nbc>0)){
-				return "1m";
-			}
-
-			if ($nbA+$nba >= $current_coverage*$MIN_VARIANTFREQUENCY){
-				if (($nbA<$MIN_FORWARDREVERSE)||($nba<$MIN_FORWARDREVERSE)){
-					return 4;
-					#  4 : variant position not covered by forward and reverse reads
-				}
-			}
-			elsif ($nbT+$nbt >= $current_coverage*$MIN_VARIANTFREQUENCY){
-				if (($nbT<$MIN_FORWARDREVERSE)||($nbt<$MIN_FORWARDREVERSE)){
-					return 4;
-					#  4 : variant position not covered by forward and reverse reads
-				}
-			}	 
-			elsif ($nbG+$nbg >= $current_coverage*$MIN_VARIANTFREQUENCY){
-				if (($nbG<$MIN_FORWARDREVERSE)||($nbg<$MIN_FORWARDREVERSE)){
-					return 4;
-					#  4 : variant position not covered by forward and reverse reads
-				}
-			}
-			elsif ($nbC+$nbc >= $current_coverage*$MIN_VARIANTFREQUENCY){
-				if (($nbC<$MIN_FORWARDREVERSE)||($nbc<$MIN_FORWARDREVERSE)){
-					return 4;
-					#  4 : variant position not covered by forward and reverse reads
-				}
-			}
-			elsif ($nbN+$nbn >= $current_coverage*$MIN_VARIANTFREQUENCY){
-				if (($nbN<$MIN_FORWARDREVERSE)||($nbn<$MIN_FORWARDREVERSE)){
-					return 4;
-					#  4 : variant position not covered by forward and reverse reads
-				}
-			}
-			else {
-				return 3;
-				#  3 : insufficient variant frequency 
-			}	
-		}
-	}
-	
-	return 0;
-}
diff -r 26d2c851d48e -r 1bf299f77ce6 mpileupfilter/mpileupfilter.xml
--- a/mpileupfilter/mpileupfilter.xml	Mon Jun 16 06:18:07 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,23 +0,0 @@
-<tool id="mpileupfilter" name="mpileupfilter" version="0.05">
-<description>Filter mpileup file entry</description>
-<command interpreter="perl">
-    mpileupfilter.pl -input_file $input_file -min_depth $min_depth -min_frequency $min_frequency -min_distance $min_distance -min_forward_and_reverse $min_forward_and_reverse -max_depth $max_depth > $output_file 
-</command>
-<inputs>
-<param name="input_file"  type="data" format="pileup" label="Select a suitable input file from your history"/>
-<param name="min_depth" type="integer" value="2" label="Minimum depth at variant position "/>
-<param name="max_depth" type="integer" value="100" label="Maximum depth at variant position "/>
-<param name="min_frequency" type="float" value="1" label="Minimum variant frequency (between 0-1 : 0.5 for 50%) "/>
-<param name="min_forward_and_reverse" type="integer" value="0" label="Minimum variant coverage by forward and reverse reads"/>
-<param name="min_distance" type="integer" value="50" label="Minimum physical distance between variant"/>
-</inputs>
-<outputs>
- <data name="output_file" format="pileup" label="${tool.name} on ${on_string}"/>
-</outputs>
-
-<help>
-
-
-
-</help>
-</tool>
diff -r 26d2c851d48e -r 1bf299f77ce6 mpileupfilteronblastxml/mpileupfilteronblastxml.pl
--- a/mpileupfilteronblastxml/mpileupfilteronblastxml.pl	Mon Jun 16 06:18:07 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,287 +0,0 @@
-#!/usr/bin/perl
-use strict;
-use warnings;
-use Getopt::Long;
-
-my $input_variant_file;
-my $input_blastxml_file;
-my $window_length = 50;
-my $nb_mismatch_max = 2;
-
-GetOptions (
-"input_variant_file=s" => \$input_variant_file,
-"input_blastxml_file=s" => \$input_blastxml_file,
-"window_length=i" => \$window_length,
-"nb_mismatch_max=i" => \$nb_mismatch_max
-) or die("Error in command line arguments\n");
-
-
-open(INB, $input_blastxml_file) or die ("Can't open $input_blastxml_file\n");
-
-
-my $iteration_stop="</Iteration>";
-my $hit_stop="</Hit>";
-my $hsp_stop="</Hsp>";
-my $query_flag_start="<Iteration_query-def>";
-my $query_flag_stop="</Iteration_query-def>";
-my $subject_flag_start="<Hit_def>";
-my $subject_flag_stop="</Hit_def>";
-my $query_HSP_flag_from_start="<Hsp_query-from>";
-my $query_HSP_flag_from_stop="</Hsp_query-from>";
-my $query_HSP_flag_to_start="<Hsp_query-to>";
-my $query_HSP_flag_to_stop="</Hsp_query-to>";
-my $subject_HSP_flag_from_start="<Hsp_hit-from>";
-my $subject_HSP_flag_from_stop="</Hsp_hit-from>";
-my $subject_HSP_flag_to_start="<Hsp_hit-to>";
-my $subject_HSP_flag_to_stop="</Hsp_hit-to>";
-my $query_HSP_flag_seq_start="<Hsp_qseq>";
-my $query_HSP_flag_seq_stop="</Hsp_qseq>";
-my $subject_HSP_flag_seq_start="<Hsp_hseq>";
-my $subject_HSP_flag_seq_stop="</Hsp_hseq>";
-my $HSP_midline_flag_start="<Hsp_midline>";
-my $HSP_midline_flag_stop="</Hsp_midline>";
-
-my %hash;
-
-my $compt=0;
-my $current_query="";
-my $current_subject="";
-my $current_HSP_query_from;
-my $current_HSP_query_to;
-my $current_HSP_subject_from;
-my $current_HSP_subject_to;
-my $current_HSP_midline;
-my $current_HSP_qseq;
-my $current_HSP_hseq;
-my $current_query_short;
-
-while (my $ligne = <INB>) {
-
-	if ($ligne=~/$subject_flag_start(.*?)$subject_flag_stop/){
-		$current_subject=$1;
-		#print "--",$1,"\n";
-	}
-	
-	if ($ligne=~/$query_flag_start(.*?)$query_flag_stop/){
-		$current_query=$1;
-		$current_query_short=$current_query;
-		if ($current_query =~ /^(.*?_\d+)\_/){
-			$current_query_short=$1;
-		}
-		if (!$hash{$current_query_short}){
-			$hash{$current_query_short}=0;
-		}
-			
-
-		#print "--",$1,"\n";
-	}
-	if ($ligne=~/$query_HSP_flag_from_start(.*?)$query_HSP_flag_from_stop/){
-		$current_HSP_query_from=$1;
-		#print "--",$1,"...";
-	}
-	if ($ligne=~/$query_HSP_flag_to_start(.*?)$query_HSP_flag_to_stop/){
-		$current_HSP_query_to=$1;
-		#print $1,"\n";
-	}
-	if ($ligne=~/$subject_HSP_flag_from_start(.*?)$subject_HSP_flag_from_stop/){
-		$current_HSP_subject_from=$1;
-		#print "--",$1,"...";
-	}
-	if ($ligne=~/$subject_HSP_flag_to_start(.*?)$subject_HSP_flag_to_stop/){
-		$current_HSP_subject_to=$1;
-		#print $1,"\n";
-	}
-	if ($ligne=~/$query_HSP_flag_seq_start(.*?)$query_HSP_flag_seq_stop/){
-		$current_HSP_qseq=$1;
-		#print "--",$1,"\n";
-	}
-	if ($ligne=~/$subject_HSP_flag_seq_start(.*?)$subject_HSP_flag_seq_stop/){
-		$current_HSP_hseq=$1;
-		#print "--",$1,"\n";
-	}
-	if ($ligne=~/$HSP_midline_flag_start(.*?)$HSP_midline_flag_stop/){
-		$current_HSP_midline=$1;
-		#print "--",$1,"\n";
-	}
-	
-	if ($ligne=~/$hsp_stop/){
-		if ($current_HSP_query_from){
-			#print "\ntest1\n";
-			#print "Query : $current_query\n";
-			#print "Subject : $current_subject\n";
-			#print "$current_HSP_query_from ... $current_HSP_query_to\n";
-			#print "$current_HSP_subject_from ... $current_HSP_subject_to\n";
-			for (my $i=1;$i<$current_HSP_query_from;$i++){
-				$current_HSP_qseq = "N".$current_HSP_qseq;
-				$current_HSP_midline = " ".$current_HSP_midline;
-				$current_HSP_hseq = "N".$current_HSP_hseq;
-			}
-			for (my $i=$current_HSP_query_to+1;$i<=$window_length*2+1;$i++){
-				$current_HSP_qseq .= "N";
-				$current_HSP_midline .= " ";
-				$current_HSP_hseq .= "N";
-			}
-			
-			my @qseq = split(//,$current_HSP_qseq);
-			my @midline = split(//,$current_HSP_midline);
-			my @hseq = split(//,$current_HSP_hseq);
-			
-			my $comptbase=0;
-			my $compt5p=0;
-			my $compt3p=0;
-			for (my $i=0;$i<=$#qseq;$i++){
-				if ($qseq[$i] ne "-"){
-					$comptbase++; # Va de 1 -> $window_length *2 +1
-				}
-				if ($midline[$i] eq " "){
-					if ($comptbase<=$window_length){ #1 -> $window_length
-						$compt5p++;
-					}
-					elsif ($comptbase>=$window_length+2){ #$window_length+2 -> $window_length *2 + 1;
-						$compt3p++;
-					}
-					else { #+1-$window_length*2+1
-						
-					}
-				}
-			}
-			if (($compt3p<=$nb_mismatch_max)||($compt5p<=$nb_mismatch_max)){
-				$hash{$current_query_short}++;
-			}
-			
-			#print "$current_HSP_qseq\n";
-			#print "$current_HSP_midline\n";
-			#print "$current_HSP_hseq\n";
-			#print "$compt5p // $compt3p\n";
-			#print $hash{$current_query_short},"\n";
-
-		}
-		
-		undef $current_HSP_query_from;
-		undef $current_HSP_query_to;
-		undef $current_HSP_subject_from;
-		undef $current_HSP_subject_to;
-		$current_HSP_midline="";
-		$current_HSP_qseq="";
-		$current_HSP_hseq="";
-	}
-	
-	if ($ligne=~/$iteration_stop/){
-		if ($current_HSP_query_from){
-			#print "\ntest2\n";
-			#print "Query : $current_query\n";
-			#print "Subject : $current_subject\n";
-			#print "$current_HSP_query_from ... $current_HSP_query_to\n";
-			#print "$current_HSP_subject_from ... $current_HSP_subject_to\n";
-			for (my $i=1;$i<$current_HSP_query_from;$i++){
-				$current_HSP_qseq = "N".$current_HSP_qseq;
-				$current_HSP_midline = " ".$current_HSP_midline;
-				$current_HSP_hseq = "N".$current_HSP_hseq;
-			}
-			for (my $i=$current_HSP_query_to+1;$i<=$window_length*2+1;$i++){
-				$current_HSP_qseq .= "N";
-				$current_HSP_midline .= " ";
-				$current_HSP_hseq .= "N";
-			}
-			
-			my @qseq = split(//,$current_HSP_qseq);
-			my @midline = split(//,$current_HSP_midline);
-			my @hseq = split(//,$current_HSP_hseq);
-			
-			my $comptbase=0;
-			my $compt5p=0;
-			my $compt3p=0;
-			for (my $i=0;$i<=$#qseq;$i++){
-				if ($qseq[$i] ne "-"){
-					$comptbase++; # Va de 1 -> $window_length *2 +1
-				}
-				if ($midline[$i] eq " "){
-					if ($comptbase<=$window_length){ #1 -> $window_length
-						$compt5p++;
-					}
-					elsif ($comptbase>=$window_length+2){ #$window_length+2 -> $window_length *2 + 1;
-						$compt3p++;
-					}
-					else { #+1-$window_length*2+1
-						
-					}
-				}
-			}
-			if (($compt3p<=$nb_mismatch_max)||($compt5p<=$nb_mismatch_max)){
-				$hash{$current_query_short}++;
-			}
-			
-			#print "$current_HSP_qseq\n";
-			#print "$current_HSP_midline\n";
-			#print "$current_HSP_hseq\n";
-			#print "$compt5p // $compt3p\n";
-			#print $hash{$current_query_short},"\n";
-		}
-		$current_query="";
-		$current_query_short="";
-		$current_subject="";
-		undef $current_HSP_query_from;
-		undef $current_HSP_query_to;
-		undef $current_HSP_subject_from;
-		undef $current_HSP_subject_to;
-		$current_HSP_midline="";
-		$current_HSP_qseq="";
-		$current_HSP_hseq="";
-	}
-	
-}
-
-close (INB);
-
-# foreach my $key (sort trinombre keys %hash){
-	# print $key," ",$hash{$key},"\n";
-	
-# }
-# exit(0);
-
-open(INV, $input_variant_file) or die ("Can't open $input_variant_file\n");
-
-while (my $ligne = <INV>) {
-	my @champs = split (/\s+/,$ligne);
-	my $header = $champs[0]."_".$champs[1];
-
-	if ($hash{$header}){
-		if ($hash{$header}==1){
-			print "$ligne";
-		}
-		else {
-			#print $hash{$header}," $ligne";
-		}
-	}
-	else {
-		print STDERR "No blast result for ",$header,"\n";
-	}
-
-	
-}
-
-close(INV);
-
-
-
-sub trinombre {
-	my $chra=$a;
-	my $posa=0;
-	my $chrb=$b;
-	my $posb=0;
-	
-	if ($a =~/(.*?)\_(\d+)/){
-		$chra=$1;
-		$posa=$2;
-	}
-	if ($b =~/(.*?)\_(\d+)/){
-		$chrb=$1;
-		$posb=$2;
-	}
-	
-	
-	$chra cmp $chrb
-	||
-	$posa <=> $posb;
-}
-
diff -r 26d2c851d48e -r 1bf299f77ce6 mpileupfilteronblastxml/mpileupfilteronblastxml.xml
--- a/mpileupfilteronblastxml/mpileupfilteronblastxml.xml	Mon Jun 16 06:18:07 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,21 +0,0 @@
-<tool id="mpileupfilteronblastxml" name="mpileupfilteronblastxml" version="0.03">
-<description>Filter mpileup with blast results</description>
-<command interpreter="perl">
-    mpileupfilteronblastxml.pl -input_variant_file $input_variant_file -input_blastxml_file $input_blastxml_file -window_length $window_length -nb_mismatch_max $nb_mismatch_max > $output_file 
-</command>
-<inputs>
-<param name="input_variant_file"  type="data" format="pileup" label="Select a suitable input VARIANT file from your history"/>
-<param name="input_blastxml_file"  type="data" format="xml" label="Select a suitable input BLASTXML file from your history"/>
-<param name="window_length" type="integer" value="50" label="Number of bases extracted before and after the variant position"/>
-<param name="nb_mismatch_max" type="integer" value="3" label="Threshold for mismatch filter"/>
-</inputs>
-<outputs>
- <data name="output_file" format="fasta" label="${tool.name} on ${on_string}"/>
-</outputs>
-
-<help>
-
-
-
-</help>
-</tool>
diff -r 26d2c851d48e -r 1bf299f77ce6 rapsodyn/Galaxy-Workflow-Pipeline_v0.1.ga
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rapsodyn/Galaxy-Workflow-Pipeline_v0.1.ga	Mon Jun 16 06:21:25 2014 -0400
@@ -0,0 +1,491 @@
+{
+    "a_galaxy_workflow": "true", 
+    "annotation": "", 
+    "format-version": "0.1", 
+    "name": "Pipeline v0.1", 
+    "steps": {
+        "0": {
+            "annotation": "", 
+            "id": 0, 
+            "input_connections": {}, 
+            "inputs": [
+                {
+                    "description": "", 
+                    "name": "Input Dataset"
+                }
+            ], 
+            "name": "Input dataset", 
+            "outputs": [], 
+            "position": {
+                "left": 200, 
+                "top": 310
+            }, 
+            "tool_errors": null, 
+            "tool_id": null, 
+            "tool_state": "{\"name\": \"Input Dataset\"}", 
+            "tool_version": null, 
+            "type": "data_input", 
+            "user_outputs": []
+        }, 
+        "1": {
+            "annotation": "", 
+            "id": 1, 
+            "input_connections": {}, 
+            "inputs": [
+                {
+                    "description": "", 
+                    "name": "Input Dataset"
+                }
+            ], 
+            "name": "Input dataset", 
+            "outputs": [], 
+            "position": {
+                "left": 205, 
+                "top": 430
+            }, 
+            "tool_errors": null, 
+            "tool_id": null, 
+            "tool_state": "{\"name\": \"Input Dataset\"}", 
+            "tool_version": null, 
+            "type": "data_input", 
+            "user_outputs": []
+        }, 
+        "2": {
+            "annotation": "", 
+            "id": 2, 
+            "input_connections": {}, 
+            "inputs": [
+                {
+                    "description": "", 
+                    "name": "Input Dataset"
+                }
+            ], 
+            "name": "Input dataset", 
+            "outputs": [], 
+            "position": {
+                "left": 904, 
+                "top": 218
+            }, 
+            "tool_errors": null, 
+            "tool_id": null, 
+            "tool_state": "{\"name\": \"Input Dataset\"}", 
+            "tool_version": null, 
+            "type": "data_input", 
+            "user_outputs": []
+        }, 
+        "3": {
+            "annotation": "", 
+            "id": 3, 
+            "input_connections": {
+                "input_file": {
+                    "id": 0, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [], 
+            "name": "FASTQ Groomer", 
+            "outputs": [
+                {
+                    "name": "output_file", 
+                    "type": "fastqsanger"
+                }
+            ], 
+            "position": {
+                "left": 354, 
+                "top": 310
+            }, 
+            "post_job_actions": {
+                "HideDatasetActionoutput_file": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "output_file"
+                }
+            }, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.0.4", 
+            "tool_state": "{\"__page__\": 0, \"input_file\": \"null\", \"input_type\": \"\\\"illumina\\\"\", \"__rerun_remap_job_id__\": null, \"options_type\": \"{\\\"options_type_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", 
+            "tool_version": "1.0.4", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "4": {
+            "annotation": "", 
+            "id": 4, 
+            "input_connections": {
+                "input_file": {
+                    "id": 1, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [], 
+            "name": "FASTQ Groomer", 
+            "outputs": [
+                {
+                    "name": "output_file", 
+                    "type": "fastqsanger"
+                }
+            ], 
+            "position": {
+                "left": 354, 
+                "top": 430
+            }, 
+            "post_job_actions": {
+                "HideDatasetActionoutput_file": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "output_file"
+                }
+            }, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.0.4", 
+            "tool_state": "{\"__page__\": 0, \"input_file\": \"null\", \"input_type\": \"\\\"illumina\\\"\", \"__rerun_remap_job_id__\": null, \"options_type\": \"{\\\"options_type_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", 
+            "tool_version": "1.0.4", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "5": {
+            "annotation": "", 
+            "id": 5, 
+            "input_connections": {
+                "readtype|input_paired1": {
+                    "id": 3, 
+                    "output_name": "output_file"
+                }, 
+                "readtype|input_paired2": {
+                    "id": 4, 
+                    "output_name": "output_file"
+                }
+            }, 
+            "inputs": [], 
+            "name": "Sickle", 
+            "outputs": [
+                {
+                    "name": "output_single", 
+                    "type": "input"
+                }, 
+                {
+                    "name": "output_paired1", 
+                    "type": "fastq"
+                }, 
+                {
+                    "name": "output_paired2", 
+                    "type": "fastq"
+                }, 
+                {
+                    "name": "output_paired_single", 
+                    "type": "fastq"
+                }
+            ], 
+            "position": {
+                "left": 574, 
+                "top": 310
+            }, 
+            "post_job_actions": {
+                "HideDatasetActionoutput_paired1": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "output_paired1"
+                }, 
+                "HideDatasetActionoutput_paired2": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "output_paired2"
+                }, 
+                "HideDatasetActionoutput_paired_single": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "output_paired_single"
+                }, 
+                "HideDatasetActionoutput_single": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "output_single"
+                }
+            }, 
+            "tool_errors": null, 
+            "tool_id": "testtoolshed.g2.bx.psu.edu/repos/jjohnson/sickle/sickle/1.0.0", 
+            "tool_state": "{\"__page__\": 0, \"length_threshold\": \"\\\"30\\\"\", \"no_five_prime\": \"\\\"False\\\"\", \"discard_n\": \"\\\"False\\\"\", \"__rerun_remap_job_id__\": null, \"readtype\": \"{\\\"single_or_paired\\\": \\\"pe\\\", \\\"input_paired1\\\": null, \\\"input_paired2\\\": null, \\\"__current_case__\\\": 1}\", \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"qual_threshold\": \"\\\"30\\\"\"}", 
+            "tool_version": "1.0.0", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "6": {
+            "annotation": "", 
+            "id": 6, 
+            "input_connections": {
+                "readtype|input_paired1": {
+                    "id": 5, 
+                    "output_name": "output_paired1"
+                }, 
+                "readtype|input_paired2": {
+                    "id": 5, 
+                    "output_name": "output_paired2"
+                }
+            }, 
+            "inputs": [], 
+            "name": "Sickle", 
+            "outputs": [
+                {
+                    "name": "output_single", 
+                    "type": "input"
+                }, 
+                {
+                    "name": "output_paired1", 
+                    "type": "fastq"
+                }, 
+                {
+                    "name": "output_paired2", 
+                    "type": "fastq"
+                }, 
+                {
+                    "name": "output_paired_single", 
+                    "type": "fastq"
+                }
+            ], 
+            "position": {
+                "left": 794, 
+                "top": 310
+            }, 
+            "post_job_actions": {
+                "HideDatasetActionoutput_paired1": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "output_paired1"
+                }, 
+                "HideDatasetActionoutput_paired2": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "output_paired2"
+                }, 
+                "HideDatasetActionoutput_paired_single": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "output_paired_single"
+                }, 
+                "HideDatasetActionoutput_single": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "output_single"
+                }
+            }, 
+            "tool_errors": null, 
+            "tool_id": "testtoolshed.g2.bx.psu.edu/repos/jjohnson/sickle/sickle/1.0.0", 
+            "tool_state": "{\"__page__\": 0, \"length_threshold\": \"\\\"30\\\"\", \"no_five_prime\": \"\\\"False\\\"\", \"discard_n\": \"\\\"True\\\"\", \"__rerun_remap_job_id__\": null, \"readtype\": \"{\\\"single_or_paired\\\": \\\"pe\\\", \\\"input_paired1\\\": null, \\\"input_paired2\\\": null, \\\"__current_case__\\\": 1}\", \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"qual_threshold\": \"\\\"30\\\"\"}", 
+            "tool_version": "1.0.0", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "7": {
+            "annotation": "", 
+            "id": 7, 
+            "input_connections": {
+                "genomeSource|ownFile": {
+                    "id": 2, 
+                    "output_name": "output"
+                }, 
+                "paired|input1": {
+                    "id": 6, 
+                    "output_name": "output_paired1"
+                }, 
+                "paired|input2": {
+                    "id": 6, 
+                    "output_name": "output_paired2"
+                }
+            }, 
+            "inputs": [], 
+            "name": "Map with BWA for Illumina", 
+            "outputs": [
+                {
+                    "name": "output", 
+                    "type": "sam"
+                }
+            ], 
+            "position": {
+                "left": 1135, 
+                "top": 363
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/bwa_wrapper/1.2.3", 
+            "tool_state": "{\"genomeSource\": \"{\\\"refGenomeSource\\\": \\\"history\\\", \\\"ownFile\\\": null, \\\"__current_case__\\\": 1}\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"paired\": \"{\\\"input2\\\": null, \\\"sPaired\\\": \\\"paired\\\", \\\"input1\\\": null, \\\"__current_case__\\\": 1}\", \"params\": \"{\\\"__current_case__\\\": 0, \\\"source_select\\\": \\\"pre_set\\\"}\", \"suppressHeader\": \"\\\"False\\\"\", \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", 
+            "tool_version": "1.2.3", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "8": {
+            "annotation": "", 
+            "id": 8, 
+            "input_connections": {
+                "input_sam_file": {
+                    "id": 7, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [], 
+            "name": "filtersamunique", 
+            "outputs": [
+                {
+                    "name": "output_file", 
+                    "type": "sam"
+                }
+            ], 
+            "position": {
+                "left": 1250, 
+                "top": 664.5
+            }, 
+            "post_job_actions": {
+                "HideDatasetActionoutput_file": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "output_file"
+                }
+            }, 
+            "tool_errors": null, 
+            "tool_id": "filtersamunique", 
+            "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_sam_file\": \"null\"}", 
+            "tool_version": "0.01", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "9": {
+            "annotation": "", 
+            "id": 9, 
+            "input_connections": {
+                "input1": {
+                    "id": 8, 
+                    "output_name": "output_file"
+                }
+            }, 
+            "inputs": [], 
+            "name": "Filter SAM or BAM", 
+            "outputs": [
+                {
+                    "name": "output1", 
+                    "type": "sam"
+                }
+            ], 
+            "position": {
+                "left": 1378, 
+                "top": 398.5
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/samtools_filter/samtools_filter/1.1.1", 
+            "tool_state": "{\"__page__\": 0, \"bed_file\": \"null\", \"input1\": \"null\", \"__rerun_remap_job_id__\": null, \"read_group\": \"\\\"\\\"\", \"library\": \"\\\"\\\"\", \"regions\": \"\\\"\\\"\", \"header\": \"\\\"-h\\\"\", \"flag\": \"{\\\"filter\\\": \\\"yes\\\", \\\"skipBits\\\": null, \\\"__current_case__\\\": 1, \\\"reqBits\\\": \\\"0x0002\\\"}\", \"mapq\": \"\\\"\\\"\"}", 
+            "tool_version": "1.1.1", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "10": {
+            "annotation": "", 
+            "id": 10, 
+            "input_connections": {
+                "source|input1": {
+                    "id": 9, 
+                    "output_name": "output1"
+                }, 
+                "source|ref_file": {
+                    "id": 2, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [], 
+            "name": "SAM-to-BAM", 
+            "outputs": [
+                {
+                    "name": "output1", 
+                    "type": "bam"
+                }
+            ], 
+            "position": {
+                "left": 1707, 
+                "top": 342
+            }, 
+            "post_job_actions": {
+                "HideDatasetActionoutput1": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "output1"
+                }
+            }, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/1.1.4", 
+            "tool_state": "{\"source\": \"{\\\"index_source\\\": \\\"history\\\", \\\"ref_file\\\": null, \\\"input1\\\": null, \\\"__current_case__\\\": 1}\", \"__rerun_remap_job_id__\": null, \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__page__\": 0}", 
+            "tool_version": "1.1.4", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "11": {
+            "annotation": "", 
+            "id": 11, 
+            "input_connections": {
+                "reference_source|input_bams_0|input_bam": {
+                    "id": 10, 
+                    "output_name": "output1"
+                }, 
+                "reference_source|ref_file": {
+                    "id": 2, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [], 
+            "name": "MPileup", 
+            "outputs": [
+                {
+                    "name": "output_mpileup", 
+                    "type": "pileup"
+                }, 
+                {
+                    "name": "output_log", 
+                    "type": "txt"
+                }
+            ], 
+            "position": {
+                "left": 1938, 
+                "top": 195
+            }, 
+            "post_job_actions": {
+                "HideDatasetActionoutput_log": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "output_log"
+                }
+            }, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/0.0.3", 
+            "tool_state": "{\"__page__\": 0, \"genotype_likelihood_computation_type\": \"{\\\"genotype_likelihood_computation_type_selector\\\": \\\"do_not_perform_genotype_likelihood_computation\\\", \\\"__current_case__\\\": 1}\", \"__rerun_remap_job_id__\": null, \"advanced_options\": \"{\\\"max_reads_per_bam\\\": \\\"250\\\", \\\"advanced_options_selector\\\": \\\"advanced\\\", \\\"extended_BAQ_computation\\\": \\\"False\\\", \\\"region_string\\\": \\\"\\\", \\\"output_per_sample_strand_bias_p_value\\\": \\\"False\\\", \\\"minimum_base_quality\\\": \\\"30\\\", \\\"disable_probabilistic_realignment\\\": \\\"False\\\", \\\"skip_anomalous_read_pairs\\\": \\\"False\\\", \\\"minimum_mapping_quality\\\": \\\"0\\\", \\\"output_per_sample_read_depth\\\": \\\"False\\\", \\\"__current_case__\\\": 0, \\\"position_list\\\": null, \\\"coefficient_for_downgrading\\\": \\\"0\\\"}\", \"reference_source\": \"{\\\"ref_file\\\": null, \\\"reference_source_selector\\\": \\\"history\\\", \\\"input_bams\\\": [{\\\"__index__\\\": 0, \\\"input_bam\\\": null}], \\\"__current_case__\\\": 1}\", \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", 
+            "tool_version": "0.0.3", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "12": {
+            "annotation": "", 
+            "id": 12, 
+            "input_connections": {
+                "input_file": {
+                    "id": 11, 
+                    "output_name": "output_mpileup"
+                }
+            }, 
+            "inputs": [], 
+            "name": "mpileupfilter", 
+            "outputs": [
+                {
+                    "name": "output_file", 
+                    "type": "pileup"
+                }
+            ], 
+            "position": {
+                "left": 2258, 
+                "top": 286.5
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "mpileupfilter", 
+            "tool_state": "{\"__page__\": 0, \"input_file\": \"null\", \"min_frequency\": \"\\\"80.0\\\"\", \"min_depth\": \"\\\"2\\\"\", \"__rerun_remap_job_id__\": null, \"min_forward_and_reverse\": \"\\\"0\\\"\", \"max_depth\": \"\\\"100\\\"\", \"min_distance\": \"\\\"0\\\"\"}", 
+            "tool_version": "0.05", 
+            "type": "tool", 
+            "user_outputs": []
+        }
+    }
+}
\ No newline at end of file
diff -r 26d2c851d48e -r 1bf299f77ce6 rapsodyn/filtersamunique/filtersamunique.pl
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rapsodyn/filtersamunique/filtersamunique.pl	Mon Jun 16 06:21:25 2014 -0400
@@ -0,0 +1,20 @@
+#!/usr/bin/perl
+use strict;
+use warnings;
+
+open(IN, $ARGV[0]) or die ("Can't open $ARGV[0]\n");
+while (my $line=<IN>){
+	if ($line =~ /^\@/){
+		#Header conservation
+		print $line;
+	}
+	else {
+		#Optionnal flag verification
+		if (($line =~ /XT\:A\:U/)&&($line =~ /X0\:i\:1/)&&($line =~ /X1\:i\:0\s/)){
+			print $line;
+		}
+	}
+}
+
+
+close (IN);
\ No newline at end of file
diff -r 26d2c851d48e -r 1bf299f77ce6 rapsodyn/filtersamunique/filtersamunique.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rapsodyn/filtersamunique/filtersamunique.xml	Mon Jun 16 06:21:25 2014 -0400
@@ -0,0 +1,18 @@
+<tool id="filtersamunique" name="filtersamunique" version="0.01">
+<description>Filter SAM file for uniquelly match reads</description>
+<command interpreter="perl">
+    filtersamunique.pl $input_sam_file > $output_file 
+</command>
+<inputs>
+<param name="input_sam_file"  type="data" format="sam" label="Select a suitable input SAM file from your history"/>
+</inputs>
+<outputs>
+ <data name="output_file" format="sam" label="${tool.name} on ${on_string}"/>
+</outputs>
+
+<help>
+
+
+
+</help>
+</tool>
diff -r 26d2c851d48e -r 1bf299f77ce6 rapsodyn/listfiltering/listfiltering.pl
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rapsodyn/listfiltering/listfiltering.pl	Mon Jun 16 06:21:25 2014 -0400
@@ -0,0 +1,61 @@
+#!/usr/bin/perl
+use strict;
+use Getopt::Long;
+
+my $inputfile;
+my $headerfile;
+my $nb_col=1;
+my %header;
+
+if ($#ARGV<0){
+	print "\n";
+	print "perl 021_ListFiltering.pl -input_file <file> -header_file <file> -nb_col <integer>[1]\n";
+	exit(0);
+}
+
+GetOptions (
+"input_file=s" => \$inputfile,
+"header_file=s" => \$headerfile,
+"nb_col=i" => \$nb_col
+) or die("Error in command line arguments\n");
+
+open(HF, $headerfile)  or die("Can't open $headerfile\n");
+while (my $line=<HF>){
+	chomp($line);
+	my @fields = split(/\s+/,$line);
+	my $ref="";
+	my $compt=0;
+	while ($compt<$nb_col){
+		if ($ref){$ref.="\t";}
+		$ref.=$fields[$compt];
+		$compt++;
+	}
+	# my $ref = "$fields[0]\t$fields[1]";
+	$header{$ref}=$line;
+}
+close (HF);
+
+
+open(IF, $inputfile)  or die("Can't open $inputfile\n");
+while (my $line=<IF>){
+	my @fields = split(/\s+/,$line);
+	my $ref="";
+	my $compt=0;
+	while ($compt<$nb_col){
+		if ($ref){$ref.="\t";}
+		$ref.=$fields[$compt];
+		$compt++;
+	}
+	# my $ref = "$fields[0]\t$fields[1]";
+
+	if ($header{$ref}){
+		# print $line;
+		# print $header{$ref},"\n";
+	}
+	else {
+		print $line;
+	}
+	
+}
+close(IF);
+
diff -r 26d2c851d48e -r 1bf299f77ce6 rapsodyn/listfiltering/listfiltering.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rapsodyn/listfiltering/listfiltering.xml	Mon Jun 16 06:21:25 2014 -0400
@@ -0,0 +1,20 @@
+<tool id="listfiltering" name="listfiltering" version="0.01">
+<description>Compare listA and listB first X column and remove from listA the elements present in listB</description>
+<command interpreter="perl">
+    listfiltering.pl -input_file $input_listA -header_file $input_listB -nb_col $nb_col > $output_file 
+</command>
+<inputs>
+<param name="input_listA"  type="data" format="pileup" label="Select a suitable input file from your history"/>
+<param name="input_listB"  type="data" format="txt" label="Select a suitable input file from your history"/>
+<param name="nb_col" type="integer" value="2" label="Number of column to compare"/>
+</inputs>
+<outputs>
+ <data name="output_file" format="pileup" label="${tool.name} on ${on_string}"/>
+</outputs>
+
+<help>
+
+
+
+</help>
+</tool>
diff -r 26d2c851d48e -r 1bf299f77ce6 rapsodyn/mpileupfilter/mpileupfilter.pl
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rapsodyn/mpileupfilter/mpileupfilter.pl	Mon Jun 16 06:21:25 2014 -0400
@@ -0,0 +1,394 @@
+#!/usr/bin/perl
+use strict;
+use Getopt::Long;
+
+#
+# Filter a pileup file on forward/reverse presence and %read having the variant
+# The error code 
+#  1 : multiple variant type detected insertion/deletion/mutation
+#  1i : inconsistency in insertion
+#  1d : inconsistency in deletion
+#  1m : inconsistency in mutation
+#  2 : insufficient depth	
+#  3 : insufficient variant frequency 
+#  4 : variant position not covered by forward and reverse reads
+#  5 : variant with other variant in neighbourhood
+#  6 : too much depth
+#  8 : parsing error (couldn't parse the mpileup line correctly)
+#  9 : parsing error (couldn't parse the readbase string correctly)
+
+
+my $inputfile;
+my $logfile;
+my $MIN_DISTANCE=0;
+my $MIN_VARIANTFREQUENCY=0;
+my $MIN_FORWARDREVERSE=0;
+my $MIN_DEPTH=0;
+my $MAX_DEPTH=500;
+my $VERBOSE=0;
+my $ONLY_UNFILTERED_VARIANT="OFF";
+
+if ($#ARGV<0){
+	print "\n";
+	print "perl 020_FilterPileupv6 -input_file <mpileup_file> [OPTION]\n";
+	print "-input_file \tinputfile in mpileup format\n";
+	print "-log_file \tlogfile containing discarded mpileup lines and the errorcode associated\n";
+	print "-min_depth \tminimum depth required [1]\n";
+	print "-max_depth \tmaximim depth (position with more coverage will be discarded) [100]\n";
+	print "-min_frequency \tminimum variant frequency (0->1) [1] (default 1 => 100% reads show the variant at this position)\n";
+	print "-min_distance \tminimum distance between variant [0]\n";
+	print "-min_forward_and_reverse \tminimum number of reads in forward and reverse covering the variant required [0]\n";
+	print "\n";
+	exit(0);
+}
+
+GetOptions (
+"input_file=s" => \$inputfile,
+"log_file=s" => \$logfile,
+"min_depth=i" => \$MIN_DEPTH,
+"max_depth=i" => \$MAX_DEPTH,
+"min_frequency=f" => \$MIN_VARIANTFREQUENCY,
+"min_distance=i" => \$MIN_DISTANCE,
+"min_forward_and_reverse=i" => \$MIN_FORWARDREVERSE,
+"variant_only=s" => \$ONLY_UNFILTERED_VARIANT,
+"v=i" => \$VERBOSE
+) or die("Error in command line arguments\n");
+
+
+open(IF, $inputfile)  or die("Can't open $inputfile\n");
+
+my @tbl_line;
+my @tbl_variant_position;
+my @tbl_variant_chr;
+my @tbl_variant_refbase;
+my @tbl_variant_coverage;
+my @tbl_variant_readbase_string;
+my @tbl_variant_quality_string;
+
+#Extraction des variants
+my $nb_line=0;
+while (my $line=<IF>){
+	$nb_line++;
+	if (($nb_line % 1000000 == 0)&&($VERBOSE==1)){
+		print "$nb_line\n";
+	}
+	my $error_code=0;
+	if ($line=~/(.*?)\s+(\d+)\s+([ATGCN])\s+(\d+)\s+(.*?)\s+(.*?)$/){
+		my $current_chromosome = $1;
+		my $current_position = $2;
+		my $current_refbase = $3;
+		my $current_coverage = $4;
+		my $current_readbase_string = $5;
+		my $current_quality_string = $6;
+		
+		#Suppression of mPileUp special character
+		$current_readbase_string =~ s/\$//g; #the read start at this position
+		$current_readbase_string =~ s/\^.//g; #the read end at this position followed by quality char
+		
+		if ($current_readbase_string =~ /[ATGCNatgcn\d]/){
+			push(@tbl_line,$line);
+			push(@tbl_variant_chr,$current_chromosome);
+			push(@tbl_variant_position,$current_position);
+			push(@tbl_variant_refbase,$current_refbase);
+			push(@tbl_variant_coverage,$current_coverage);
+			push(@tbl_variant_readbase_string,$current_readbase_string);
+			push(@tbl_variant_quality_string,$current_quality_string);
+			if ($ONLY_UNFILTERED_VARIANT eq "ON"){
+				print $line;
+			}
+			
+		}
+		else {
+			#Position with no variant
+		}
+		
+	}
+	else {
+		#Error Parsing
+		print STDERR "$line #8";
+	}
+}
+close(IF);
+
+if ($ONLY_UNFILTERED_VARIANT eq "ON"){
+	exit(0);
+}
+
+####Checking the distance between variant and other filter
+
+if ($logfile){
+	open(LF,">$logfile") or die ("Cant't open $logfile\n");
+}
+
+for (my $i=0;$i<=$#tbl_line;$i++){
+	# print "ligne : $tbl_line[$i]\n";
+				
+	my $error_code=0;
+	if ($i==0){
+		#Comparing $i and $i+1 for neighbourhood filter;
+		if ($#tbl_line>0){
+			if (($tbl_variant_chr[$i+1] eq $tbl_variant_chr[$i])&&($tbl_variant_position[$i]+$MIN_DISTANCE>=$tbl_variant_position[$i+1])){
+				$error_code=5;
+				chomp($tbl_line[$i]);
+				if ($logfile){
+					print LF "$tbl_line[$i]\tcode:$error_code\n";
+				}
+				next;
+			}
+		}
+
+		#Additionnal filters
+		$error_code = check_error($tbl_variant_chr[$i],$tbl_variant_position[$i],$tbl_variant_refbase[$i],$tbl_variant_coverage[$i],$tbl_variant_readbase_string[$i]);
+
+	}
+	else {
+		#Compairing $i and $i-1 for neighbourhood filter
+		if (($tbl_variant_chr[$i-1] eq $tbl_variant_chr[$i])&&($tbl_variant_position[$i-1]+$MIN_DISTANCE>=$tbl_variant_position[$i])){
+			$error_code=5;
+			chomp($tbl_line[$i]);
+			if ($logfile){
+				print LF "$tbl_line[$i]\tcode:$error_code\n";
+			}
+			next;
+		}
+		else {
+			#Additionnal filters
+			$error_code = check_error($tbl_variant_chr[$i],$tbl_variant_position[$i],$tbl_variant_refbase[$i],$tbl_variant_coverage[$i],$tbl_variant_readbase_string[$i]);
+		}
+	}
+	if ($error_code == 0){
+		print $tbl_line[$i];
+	}
+	else {
+		chomp($tbl_line[$i]);
+		if ($logfile){
+			print LF "$tbl_line[$i]\tcode:$error_code\n";
+		}
+	}
+}
+
+if ($logfile){
+	close (LF);
+}
+
+sub check_error{
+	my $current_chromosome = shift;
+	my $current_position = shift;
+	my $current_refbase = shift;
+	my $current_coverage = shift;
+	my $current_readbase_string = shift;
+	
+	# print "test : $current_readbase_string\n";
+	
+
+	
+	#Extraction of insertions
+	
+	##################################################################
+	# my @IN = $current_readbase_string =~ m/\+[0-9]+[ACGTNacgtn]+/g;
+	# my @DEL = $current_readbase_string =~ m/\-[0-9]+[ACGTNacgtn]+/g;
+	# print "IN : @IN\n";
+	# print "DEL :@DEL\n";
+	#$current_readbase_string=~s/[\+\-][0-9]+[ACGTNacgtn]+//g; 
+	##################################################################
+	#!!! marche pas : exemple .+1Ct. correspond a . / +1C / t /. mais le match de l'expression vire +1Ct
+	##################################################################
+	
+	# => parcours de boucle
+	my @readbase = split(//,$current_readbase_string);
+	my $cleaned_readbase_string="";
+	my @IN;
+	my @DEL;
+	my $current_IN="";
+	my $current_DEL="";
+	my $current_size=0;
+	
+	for (my $i=0;$i<=$#readbase;$i++){
+		if ($readbase[$i] eq "+"){
+			#Ouverture de IN
+			$current_IN="+";
+			
+			#Recuperation de la taille
+			my $sub = substr $current_readbase_string,$i;
+			if ($sub=~/^\+(\d+)/){
+				$current_size = $1;
+			}
+			my $remaining_size = $current_size;
+			while (($remaining_size>0)&&($i<=$#readbase)){
+				$i++;
+				$current_IN.=$readbase[$i];
+				if ($readbase[$i]=~ /[ATGCNatgcn]/){
+					$remaining_size--;
+				}
+			}
+			push(@IN,$current_IN);
+		}
+		elsif ($readbase[$i] eq "-"){
+			#Ouverture de DEL
+			$current_DEL="-";
+			
+			#Recuperation de la taille
+			my $sub = substr $current_readbase_string,$i;
+			if ($sub=~/^\-(\d+)/){
+				$current_size = $1;
+			}
+			my $remaining_size = $current_size;
+			while (($remaining_size>0)&&($i<=$#readbase)){
+				$i++;
+				$current_DEL.=$readbase[$i];
+				if ($readbase[$i]=~ /[ATGCNatgcn]/){
+					$remaining_size--;
+				}
+			}
+			push(@DEL,$current_DEL);
+			
+		}
+		else {
+			#Ajout a la string
+			$cleaned_readbase_string .= $readbase[$i];
+		}
+	}
+
+	
+	# print "IN : @IN\n";
+	# print "DEL :@DEL\n";
+	# print "$cleaned_readbase_string\n";	
+	
+	my @current_readbase_array = split(//,$cleaned_readbase_string);
+
+	#Filtering : error detection
+
+	if ($#current_readbase_array+1 != $current_coverage){
+		return 9;
+		#parsing error (couldn't parse the readbase string correctly)
+	}
+	elsif ($current_coverage<$MIN_DEPTH){
+		return 2;
+		#  2 : insufficient depth
+	}
+	elsif ($current_coverage>$MAX_DEPTH){
+		return 6;
+		#  6 : too much depth
+	}
+	else {
+		if ($#IN>=0){
+			if (($cleaned_readbase_string=~/[ACGTNacgtn]/)){
+				return 1;
+				#  1 : variant type overload (multiple variant type detected insertion/deletion/mutation)
+			}
+			else {
+				########## TEST de coherence des insertions ################
+				# for (my $i=0;$i<=$#IN;$i++){
+					# if (uc($IN[0]) ne uc($IN[$i])){
+						# print uc($IN[0]),"\n";
+						# print uc($IN[$i]),"\n";
+						# return "1i";
+					# }
+				# }		
+				###########################################################
+
+				if($#IN+1 < $current_coverage*$MIN_VARIANTFREQUENCY){
+					return 3;
+					#  3 : insufficient variant frequency 
+				}
+			}
+		}
+		elsif ($#DEL>=0){
+			if (($cleaned_readbase_string=~/[ACGTNacgtn]/)){
+				return 1;
+				#  1 : variant type overload (multiple variant type detected insertion/deletion/mutation)
+			}
+			else {
+				########## TEST de coherence des deletions ################
+				# for (my $i=0;$i<=$#DEL;$i++){
+					# if (uc($DEL[0]) ne uc($DEL[$i])){
+						# print uc($DEL[0]),"\n";
+						# print uc($DEL[$i]),"\n";
+						# return "1d";
+					# }
+				# }
+				###########################################################
+
+				if($#DEL+1 < $current_coverage*$MIN_VARIANTFREQUENCY){
+					return 3;
+					#  3 : insufficient variant frequency 
+				}
+			}
+		}
+		else {
+			my $nbA=0;
+			$nbA++ while ($current_readbase_string =~ m/A/g);
+			my $nbC=0;
+			$nbC++ while ($current_readbase_string =~ m/C/g);
+			my $nbT=0;
+			$nbT++ while ($current_readbase_string =~ m/T/g);
+			my $nbG=0;
+			$nbG++ while ($current_readbase_string =~ m/G/g);
+			my $nbN=0;
+			$nbN++ while ($current_readbase_string =~ m/N/g);
+			my $nba=0;
+			$nba++ while ($current_readbase_string =~ m/a/g);
+			my $nbc=0;
+			$nbc++ while ($current_readbase_string =~ m/c/g);
+			my $nbt=0;
+			$nbt++ while ($current_readbase_string =~ m/t/g);
+			my $nbg=0;
+			$nbg++ while ($current_readbase_string =~ m/g/g);
+			my $nbn=0;
+			$nbn++ while ($current_readbase_string =~ m/n/g);
+
+			if (($nbA+$nba>0)&&($nbT+$nbt+$nbG+$nbg+$nbC+$nbc+$nbN+$nbn>0)){
+				return "1m";
+			}
+			if (($nbT+$nbt>0)&&($nbA+$nba+$nbG+$nbg+$nbC+$nbc+$nbN+$nbn>0)){
+				return "1m";
+			}
+			if (($nbG+$nbg>0)&&($nbA+$nba+$nbT+$nbt+$nbC+$nbc+$nbN+$nbn>0)){
+				return "1m";
+			}
+			if (($nbC+$nbc>0)&&($nbA+$nba+$nbT+$nbt+$nbG+$nbg+$nbN+$nbn>0)){
+				return "1m";
+			}
+			if (($nbN+$nbn>0)&&($nbA+$nba+$nbT+$nbt+$nbG+$nbg+$nbC+$nbc>0)){
+				return "1m";
+			}
+
+			if ($nbA+$nba >= $current_coverage*$MIN_VARIANTFREQUENCY){
+				if (($nbA<$MIN_FORWARDREVERSE)||($nba<$MIN_FORWARDREVERSE)){
+					return 4;
+					#  4 : variant position not covered by forward and reverse reads
+				}
+			}
+			elsif ($nbT+$nbt >= $current_coverage*$MIN_VARIANTFREQUENCY){
+				if (($nbT<$MIN_FORWARDREVERSE)||($nbt<$MIN_FORWARDREVERSE)){
+					return 4;
+					#  4 : variant position not covered by forward and reverse reads
+				}
+			}	 
+			elsif ($nbG+$nbg >= $current_coverage*$MIN_VARIANTFREQUENCY){
+				if (($nbG<$MIN_FORWARDREVERSE)||($nbg<$MIN_FORWARDREVERSE)){
+					return 4;
+					#  4 : variant position not covered by forward and reverse reads
+				}
+			}
+			elsif ($nbC+$nbc >= $current_coverage*$MIN_VARIANTFREQUENCY){
+				if (($nbC<$MIN_FORWARDREVERSE)||($nbc<$MIN_FORWARDREVERSE)){
+					return 4;
+					#  4 : variant position not covered by forward and reverse reads
+				}
+			}
+			elsif ($nbN+$nbn >= $current_coverage*$MIN_VARIANTFREQUENCY){
+				if (($nbN<$MIN_FORWARDREVERSE)||($nbn<$MIN_FORWARDREVERSE)){
+					return 4;
+					#  4 : variant position not covered by forward and reverse reads
+				}
+			}
+			else {
+				return 3;
+				#  3 : insufficient variant frequency 
+			}	
+		}
+	}
+	
+	return 0;
+}
diff -r 26d2c851d48e -r 1bf299f77ce6 rapsodyn/mpileupfilter/mpileupfilter.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rapsodyn/mpileupfilter/mpileupfilter.xml	Mon Jun 16 06:21:25 2014 -0400
@@ -0,0 +1,23 @@
+<tool id="mpileupfilter" name="mpileupfilter" version="0.05">
+<description>Filter mpileup file entry</description>
+<command interpreter="perl">
+    mpileupfilter.pl -input_file $input_file -min_depth $min_depth -min_frequency $min_frequency -min_distance $min_distance -min_forward_and_reverse $min_forward_and_reverse -max_depth $max_depth > $output_file 
+</command>
+<inputs>
+<param name="input_file"  type="data" format="pileup" label="Select a suitable input file from your history"/>
+<param name="min_depth" type="integer" value="2" label="Minimum depth at variant position "/>
+<param name="max_depth" type="integer" value="100" label="Maximum depth at variant position "/>
+<param name="min_frequency" type="float" value="1" label="Minimum variant frequency (between 0-1 : 0.5 for 50%) "/>
+<param name="min_forward_and_reverse" type="integer" value="0" label="Minimum variant coverage by forward and reverse reads"/>
+<param name="min_distance" type="integer" value="50" label="Minimum physical distance between variant"/>
+</inputs>
+<outputs>
+ <data name="output_file" format="pileup" label="${tool.name} on ${on_string}"/>
+</outputs>
+
+<help>
+
+
+
+</help>
+</tool>
diff -r 26d2c851d48e -r 1bf299f77ce6 rapsodyn/mpileupfilteronblastxml/mpileupfilteronblastxml.pl
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rapsodyn/mpileupfilteronblastxml/mpileupfilteronblastxml.pl	Mon Jun 16 06:21:25 2014 -0400
@@ -0,0 +1,287 @@
+#!/usr/bin/perl
+use strict;
+use warnings;
+use Getopt::Long;
+
+my $input_variant_file;
+my $input_blastxml_file;
+my $window_length = 50;
+my $nb_mismatch_max = 2;
+
+GetOptions (
+"input_variant_file=s" => \$input_variant_file,
+"input_blastxml_file=s" => \$input_blastxml_file,
+"window_length=i" => \$window_length,
+"nb_mismatch_max=i" => \$nb_mismatch_max
+) or die("Error in command line arguments\n");
+
+
+open(INB, $input_blastxml_file) or die ("Can't open $input_blastxml_file\n");
+
+
+my $iteration_stop="</Iteration>";
+my $hit_stop="</Hit>";
+my $hsp_stop="</Hsp>";
+my $query_flag_start="<Iteration_query-def>";
+my $query_flag_stop="</Iteration_query-def>";
+my $subject_flag_start="<Hit_def>";
+my $subject_flag_stop="</Hit_def>";
+my $query_HSP_flag_from_start="<Hsp_query-from>";
+my $query_HSP_flag_from_stop="</Hsp_query-from>";
+my $query_HSP_flag_to_start="<Hsp_query-to>";
+my $query_HSP_flag_to_stop="</Hsp_query-to>";
+my $subject_HSP_flag_from_start="<Hsp_hit-from>";
+my $subject_HSP_flag_from_stop="</Hsp_hit-from>";
+my $subject_HSP_flag_to_start="<Hsp_hit-to>";
+my $subject_HSP_flag_to_stop="</Hsp_hit-to>";
+my $query_HSP_flag_seq_start="<Hsp_qseq>";
+my $query_HSP_flag_seq_stop="</Hsp_qseq>";
+my $subject_HSP_flag_seq_start="<Hsp_hseq>";
+my $subject_HSP_flag_seq_stop="</Hsp_hseq>";
+my $HSP_midline_flag_start="<Hsp_midline>";
+my $HSP_midline_flag_stop="</Hsp_midline>";
+
+my %hash;
+
+my $compt=0;
+my $current_query="";
+my $current_subject="";
+my $current_HSP_query_from;
+my $current_HSP_query_to;
+my $current_HSP_subject_from;
+my $current_HSP_subject_to;
+my $current_HSP_midline;
+my $current_HSP_qseq;
+my $current_HSP_hseq;
+my $current_query_short;
+
+while (my $ligne = <INB>) {
+
+	if ($ligne=~/$subject_flag_start(.*?)$subject_flag_stop/){
+		$current_subject=$1;
+		#print "--",$1,"\n";
+	}
+	
+	if ($ligne=~/$query_flag_start(.*?)$query_flag_stop/){
+		$current_query=$1;
+		$current_query_short=$current_query;
+		if ($current_query =~ /^(.*?_\d+)\_/){
+			$current_query_short=$1;
+		}
+		if (!$hash{$current_query_short}){
+			$hash{$current_query_short}=0;
+		}
+			
+
+		#print "--",$1,"\n";
+	}
+	if ($ligne=~/$query_HSP_flag_from_start(.*?)$query_HSP_flag_from_stop/){
+		$current_HSP_query_from=$1;
+		#print "--",$1,"...";
+	}
+	if ($ligne=~/$query_HSP_flag_to_start(.*?)$query_HSP_flag_to_stop/){
+		$current_HSP_query_to=$1;
+		#print $1,"\n";
+	}
+	if ($ligne=~/$subject_HSP_flag_from_start(.*?)$subject_HSP_flag_from_stop/){
+		$current_HSP_subject_from=$1;
+		#print "--",$1,"...";
+	}
+	if ($ligne=~/$subject_HSP_flag_to_start(.*?)$subject_HSP_flag_to_stop/){
+		$current_HSP_subject_to=$1;
+		#print $1,"\n";
+	}
+	if ($ligne=~/$query_HSP_flag_seq_start(.*?)$query_HSP_flag_seq_stop/){
+		$current_HSP_qseq=$1;
+		#print "--",$1,"\n";
+	}
+	if ($ligne=~/$subject_HSP_flag_seq_start(.*?)$subject_HSP_flag_seq_stop/){
+		$current_HSP_hseq=$1;
+		#print "--",$1,"\n";
+	}
+	if ($ligne=~/$HSP_midline_flag_start(.*?)$HSP_midline_flag_stop/){
+		$current_HSP_midline=$1;
+		#print "--",$1,"\n";
+	}
+	
+	if ($ligne=~/$hsp_stop/){
+		if ($current_HSP_query_from){
+			#print "\ntest1\n";
+			#print "Query : $current_query\n";
+			#print "Subject : $current_subject\n";
+			#print "$current_HSP_query_from ... $current_HSP_query_to\n";
+			#print "$current_HSP_subject_from ... $current_HSP_subject_to\n";
+			for (my $i=1;$i<$current_HSP_query_from;$i++){
+				$current_HSP_qseq = "N".$current_HSP_qseq;
+				$current_HSP_midline = " ".$current_HSP_midline;
+				$current_HSP_hseq = "N".$current_HSP_hseq;
+			}
+			for (my $i=$current_HSP_query_to+1;$i<=$window_length*2+1;$i++){
+				$current_HSP_qseq .= "N";
+				$current_HSP_midline .= " ";
+				$current_HSP_hseq .= "N";
+			}
+			
+			my @qseq = split(//,$current_HSP_qseq);
+			my @midline = split(//,$current_HSP_midline);
+			my @hseq = split(//,$current_HSP_hseq);
+			
+			my $comptbase=0;
+			my $compt5p=0;
+			my $compt3p=0;
+			for (my $i=0;$i<=$#qseq;$i++){
+				if ($qseq[$i] ne "-"){
+					$comptbase++; # Va de 1 -> $window_length *2 +1
+				}
+				if ($midline[$i] eq " "){
+					if ($comptbase<=$window_length){ #1 -> $window_length
+						$compt5p++;
+					}
+					elsif ($comptbase>=$window_length+2){ #$window_length+2 -> $window_length *2 + 1;
+						$compt3p++;
+					}
+					else { #+1-$window_length*2+1
+						
+					}
+				}
+			}
+			if (($compt3p<=$nb_mismatch_max)||($compt5p<=$nb_mismatch_max)){
+				$hash{$current_query_short}++;
+			}
+			
+			#print "$current_HSP_qseq\n";
+			#print "$current_HSP_midline\n";
+			#print "$current_HSP_hseq\n";
+			#print "$compt5p // $compt3p\n";
+			#print $hash{$current_query_short},"\n";
+
+		}
+		
+		undef $current_HSP_query_from;
+		undef $current_HSP_query_to;
+		undef $current_HSP_subject_from;
+		undef $current_HSP_subject_to;
+		$current_HSP_midline="";
+		$current_HSP_qseq="";
+		$current_HSP_hseq="";
+	}
+	
+	if ($ligne=~/$iteration_stop/){
+		if ($current_HSP_query_from){
+			#print "\ntest2\n";
+			#print "Query : $current_query\n";
+			#print "Subject : $current_subject\n";
+			#print "$current_HSP_query_from ... $current_HSP_query_to\n";
+			#print "$current_HSP_subject_from ... $current_HSP_subject_to\n";
+			for (my $i=1;$i<$current_HSP_query_from;$i++){
+				$current_HSP_qseq = "N".$current_HSP_qseq;
+				$current_HSP_midline = " ".$current_HSP_midline;
+				$current_HSP_hseq = "N".$current_HSP_hseq;
+			}
+			for (my $i=$current_HSP_query_to+1;$i<=$window_length*2+1;$i++){
+				$current_HSP_qseq .= "N";
+				$current_HSP_midline .= " ";
+				$current_HSP_hseq .= "N";
+			}
+			
+			my @qseq = split(//,$current_HSP_qseq);
+			my @midline = split(//,$current_HSP_midline);
+			my @hseq = split(//,$current_HSP_hseq);
+			
+			my $comptbase=0;
+			my $compt5p=0;
+			my $compt3p=0;
+			for (my $i=0;$i<=$#qseq;$i++){
+				if ($qseq[$i] ne "-"){
+					$comptbase++; # Va de 1 -> $window_length *2 +1
+				}
+				if ($midline[$i] eq " "){
+					if ($comptbase<=$window_length){ #1 -> $window_length
+						$compt5p++;
+					}
+					elsif ($comptbase>=$window_length+2){ #$window_length+2 -> $window_length *2 + 1;
+						$compt3p++;
+					}
+					else { #+1-$window_length*2+1
+						
+					}
+				}
+			}
+			if (($compt3p<=$nb_mismatch_max)||($compt5p<=$nb_mismatch_max)){
+				$hash{$current_query_short}++;
+			}
+			
+			#print "$current_HSP_qseq\n";
+			#print "$current_HSP_midline\n";
+			#print "$current_HSP_hseq\n";
+			#print "$compt5p // $compt3p\n";
+			#print $hash{$current_query_short},"\n";
+		}
+		$current_query="";
+		$current_query_short="";
+		$current_subject="";
+		undef $current_HSP_query_from;
+		undef $current_HSP_query_to;
+		undef $current_HSP_subject_from;
+		undef $current_HSP_subject_to;
+		$current_HSP_midline="";
+		$current_HSP_qseq="";
+		$current_HSP_hseq="";
+	}
+	
+}
+
+close (INB);
+
+# foreach my $key (sort trinombre keys %hash){
+	# print $key," ",$hash{$key},"\n";
+	
+# }
+# exit(0);
+
+open(INV, $input_variant_file) or die ("Can't open $input_variant_file\n");
+
+while (my $ligne = <INV>) {
+	my @champs = split (/\s+/,$ligne);
+	my $header = $champs[0]."_".$champs[1];
+
+	if ($hash{$header}){
+		if ($hash{$header}==1){
+			print "$ligne";
+		}
+		else {
+			#print $hash{$header}," $ligne";
+		}
+	}
+	else {
+		print STDERR "No blast result for ",$header,"\n";
+	}
+
+	
+}
+
+close(INV);
+
+
+
+sub trinombre {
+	my $chra=$a;
+	my $posa=0;
+	my $chrb=$b;
+	my $posb=0;
+	
+	if ($a =~/(.*?)\_(\d+)/){
+		$chra=$1;
+		$posa=$2;
+	}
+	if ($b =~/(.*?)\_(\d+)/){
+		$chrb=$1;
+		$posb=$2;
+	}
+	
+	
+	$chra cmp $chrb
+	||
+	$posa <=> $posb;
+}
+
diff -r 26d2c851d48e -r 1bf299f77ce6 rapsodyn/mpileupfilteronblastxml/mpileupfilteronblastxml.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rapsodyn/mpileupfilteronblastxml/mpileupfilteronblastxml.xml	Mon Jun 16 06:21:25 2014 -0400
@@ -0,0 +1,21 @@
+<tool id="mpileupfilteronblastxml" name="mpileupfilteronblastxml" version="0.03">
+<description>Filter mpileup with blast results</description>
+<command interpreter="perl">
+    mpileupfilteronblastxml.pl -input_variant_file $input_variant_file -input_blastxml_file $input_blastxml_file -window_length $window_length -nb_mismatch_max $nb_mismatch_max > $output_file 
+</command>
+<inputs>
+<param name="input_variant_file"  type="data" format="pileup" label="Select a suitable input VARIANT file from your history"/>
+<param name="input_blastxml_file"  type="data" format="xml" label="Select a suitable input BLASTXML file from your history"/>
+<param name="window_length" type="integer" value="50" label="Number of bases extracted before and after the variant position"/>
+<param name="nb_mismatch_max" type="integer" value="3" label="Threshold for mismatch filter"/>
+</inputs>
+<outputs>
+ <data name="output_file" format="fasta" label="${tool.name} on ${on_string}"/>
+</outputs>
+
+<help>
+
+
+
+</help>
+</tool>