changeset 1:3203097d0a70 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/perl/lib/Fasta.pm	Thu Oct 15 09:53:48 2015 -0400
@@ -0,0 +1,314 @@
+package Tools::Fasta;
+
+use strict;
+use warnings;
+use Logger::Logger;
+use Data::Dumper;
+use Storable;
+
+=head1 INDEXED FASTA RELATED METHODS
+
+=head2
+
+=head2 new
+
+=head2
+
+=head3 Description
+
+Create a new Tools::Fasta object and index the FASTA file
+
+=head3 Arguments
+
+=over 4
+
+=item
+
+A hash of parameters.
+
+Currently accepted keys are :
+
+'file' => FASTA file path
+
+=back
+
+=head3 Returns
+
+=over 4
+
+=item
+
+A Tools::Fasta object
+
+=back
+
+=cut
+
+sub new {
+	my ($class, %attrs) = @_;
+	my $self = {};
+	bless $self;
+	if(defined($attrs{file})){
+		$self->{file} = $attrs{file};
+		open($self->{file_handle},$self->{file}) || $logger->logdie('Error opening file : '. $self->{file}.' : '.$!."\n");
+		$self->indexFastaFile;
+	}
+	return $self;
+}
+
+=head2 indexFastaFile
+
+=head2
+
+=head3 Description
+
+Index a FASTA file creating a hash reference with the following structure :
+
+$index -> {seq_id} = {'id_begin_position' => integer, 'sequence_end_position' => integer, 'description' => string, 'position' => integer}
+
+For each sequence id, the ">" symbol and all the text after space will be removed.
+
+This cleaned id will be used as key for the index.
+
+=head3 Arguments
+
+=over 4
+
+=item
+
+None
+
+=back
+
+=head3 Returns
+
+=over 4
+
+=item
+
+None
+
+=back
+
+=cut
+
+sub indexFastaFile {
+	my ($self) = @_;
+  $logger->info('Indexing file : '.$self->{file}."\n");
+  my $id;
+  my $id_begin_position = 0;
+  my $description;
+	my $pos=0;
+	my $fh = $self->{file_handle};
+  while(my $line = <$fh>){
+    if($line =~ /^>(\S+)\s?(.*)$/){
+      $id = $1;
+      $description = $2;
+			$pos++;
+      $self->{index}->{$id} = {'id_begin_position' => $id_begin_position, 'sequence_end_position' => 0, 'description' => $description, 'position' => $pos};
+    }
+    else{
+      $self->{index}->{$id}{'sequence_end_position'} += length $line;
+			$logger->trace('TRACE: Indexing sequence' . $id . ' (id_begin_position : '. $self->{index}->{$id}{'id_begin_position'} . ', sequence_end_position : '. $self->{index}->{$id}{'sequence_end_position'} .') from ' . $self->{file} . "\n");
+    }
+    $id_begin_position = tell($fh);
+  }
+  $logger->info('File '.$self->{file}.' is now indexed (index contains '.(scalar keys %{$self->{index}})." sequences)\n");
+}
+
+=head2 loadFastaIndexFile
+
+=head2
+
+=head3 Description
+
+Retrieve index from file using Storable module
+
+=head3 Arguments
+
+=over 4
+
+An index file
+
+=back
+
+=head3 Returns
+
+=over 4
+
+=item
+
+A hash reference corresponding to the index of the input FASTA file :
+
+$index -> {seq_id} = {'id_begin_position' => integer, 'sequence_end_position' => integer, 'description' => string, 'position' => integer}
+
+=back
+
+=cut
+
+sub loadFastaIndexFile {
+	my ($self,$file) = @_;
+  $self->{index} = retrieve($file);
+	return $self->{index};
+}
+
+=head2 writeFastaIndexFile
+
+=head2
+
+=head3 Description
+
+Write index to file using Storable module
+
+=head3 Arguments
+
+=over 4
+
+=item
+
+A hash reference corresponding to FASTA index.
+
+=item
+
+An output file path where to store the index.
+
+=back
+
+=head3 Returns
+
+=over 4
+
+=item
+
+The output file path containing index
+
+=back
+
+=cut
+
+sub writeFastaIndexFile {
+	my ($self,$file) = @_;
+  $logger->info('Writing index ('.(scalar keys %{$self->{index}}).' sequences) in file : '.$file."\n");
+  store $self->{index}, $file;
+  $logger->info('File '.$file." is now created\n");
+	return $file;
+}
+
+=head2 retrieveFastaSequence
+
+=head2
+
+=head3 Description
+
+Retrieve FASTA sequences using a list of ids
+
+=head3 Arguments
+
+=over 4
+
+=item
+
+A sequence id OR an array reference containing the list of sequences id to retrieve.
+
+=back
+
+=head3 Returns
+
+=over 4
+
+=item
+
+A hash reference containing sequences id as keys and sequences as values
+
+$data -> {seq_id} = sequence_corresponding_to_seq_id
+
+=back
+
+=cut
+
+sub retrieveFastaSequence {
+	my ($self,$ids) = @_;
+	my $data;
+  my $nbSequences = 0;
+	my $fh = $self->{file_handle};
+  if(! ref $ids){$ids = [$ids]}
+  $logger->debug('Retrieving sequences of ids ['.join(', ', @$ids).'] from indexed file : '.$self->{file}."\n");
+  foreach my $id (@$ids){
+		my $cleanedId = $id;
+		if($id =~ /^>?(\S*)/){$cleanedId = $1}
+      $logger->trace('DEBUG: retrieving informations of id ' . $cleanedId. " from index\n");
+      if(exists $self->{index}->{$cleanedId}){
+        $logger->trace('DEBUG: id ' . $cleanedId . ' is present in index (id_begin_position : '. $self->{index}->{$cleanedId}{'id_begin_position'}. ', sequence_end_position : '. $self->{index}->{$cleanedId}{'sequence_end_position'}.")\n");
+        seek($fh, $self->{index}->{$cleanedId}{'id_begin_position'}, 0);
+        my $sequence = <$fh>;
+        read($fh, $sequence, $self->{index}->{$cleanedId}{'sequence_end_position'});
+        $sequence =~ s/\n//g;
+      	$data->{$id} = $sequence;
+        $nbSequences++;
+			}
+    	else{
+				$logger->trace('DEBUG: id ' . $cleanedId. " not found in index\n");
+			}
+	}
+  $logger->trace($nbSequences.'/'.scalar(@$ids).' sequences has been retrieved from indexed file ' . $self->{file} . "\n");
+	return $data;
+}
+
+=head2 retrieveFastaBlock
+
+=head2
+
+=head3 Description
+
+Retrieve FASTA formatted sequences using a list of ids
+
+=head3 Arguments
+
+=over 4
+
+=item
+
+A sequence id OR an array reference containing the list of sequences id to retrieve.
+
+=back
+
+=head3 Returns
+
+=over 4
+
+=item
+
+A scalar containing the sequences corresponding to ids in FASTA format
+
+=back
+
+=cut
+
+sub retrieveFastaBlock {
+	my ($self,$ids) = @_;
+	my $data;
+  my $nbSequences = 0;
+	my $fh = $self->{file_handle};
+  if(! ref $ids){$ids = [$ids]}
+	$logger->debug('Retrieving fasta block of ' . scalar(@$ids) . ' ids from indexed file : '.$self->{file}."\n");
+  foreach my $id (@$ids){
+		my $cleanedId = $id;
+		if($id =~ /^>?(\S*)/){$cleanedId = $1}
+  	$logger->trace('TRACE: retrieving informations of id ' . $cleanedId. " from index\n");
+    if(exists $self->{index}->{$cleanedId}){
+      $logger->trace('TRACE: id ' . $cleanedId . ' is present in index (id_begin_position : '. $self->{index}->{$cleanedId}{'id_begin_position'}. ', sequence_end_position : '. $self->{index}->{$cleanedId}{'sequence_end_position'}.")\n");
+      seek($fh, $self->{index}->{$cleanedId}{'id_begin_position'}, 0);
+      my $blockId = <$fh>;
+      read($fh, my $sequence, $self->{index}->{$cleanedId}{'sequence_end_position'});
+    	$data .= $blockId . $sequence . "\n";
+      $nbSequences++;
+      $logger->trace('TRACE: fasta block of id ' . $cleanedId . ' is : ' . "\n" . $blockId.$sequence . "\n")
+    }
+    else{
+			$logger->warn('WARN: id ' . $cleanedId. " not found in index\n");
+		}
+	}
+  $logger->debug($nbSequences . '/' . scalar(@$ids) . ' fasta block has been retrieved from indexed file ' . $self->{file} . "\n");
+	return $data;
+}
+1;

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/perl/lib/Fastq.pm	Thu Oct 15 09:53:48 2015 -0400
@@ -0,0 +1,382 @@
+package Tools::Fastq;
+
+use strict;
+use warnings;
+use Logger::Logger;
+use Storable;
+
+
+=head1 INDEXED FASTQ RELATED METHODS
+
+=head2
+
+=head2 new
+
+=head2
+
+=head3 Description
+
+Create a new Tools::Fastq object and index the FASTQ file
+
+=head3 Arguments
+
+=over 4
+
+=item
+
+A hash of parameters.
+
+Currently accepted keys are :
+
+'file' => FASTQ file path
+
+=back
+
+=head3 Returns
+
+=over 4
+
+=item
+
+A Tools::Fastq object
+
+=back
+
+=cut
+
+sub new {
+	my ($class, %attrs) = @_;
+	my $self = {};
+	bless $self;
+	if(defined($attrs{file})){
+		$self->{file} = $attrs{file};
+		open($self->{file_handle},$self->{file}) || $logger->logdie('Error opening file : '. $self->{file}.' : '.$!."\n");
+		$self->indexFastqFile;
+	}
+	return $self;
+}
+
+=head2 indexFastqFile
+
+=head2
+
+=head3 Description
+
+Index a FASTQ file creating a hash reference with the following structure :
+
+$index -> {seq_id} = {'id_begin_position' => integer, 'id_length' => integer}
+
+For each sequence id, the "@" symbol and all the text after space will be removed.
+
+This cleaned id will be used as key for the index.
+
+=head3 Arguments
+
+=over 4
+
+=item
+
+None
+
+=back
+
+=head3 Returns
+
+=over 4
+
+=item
+
+None
+
+=back
+
+=cut
+
+sub indexFastqFile{
+
+	  my ($self) = @_;
+    $logger->info('Indexing file : '.$self->{file}."\n");
+    my $index;
+    my $id;
+    my $id_begin_position = 0;
+		my $fh = $self->{file_handle};
+    while(my $line = <$fh>){
+
+        if($line =~ /^@(\S+)/){
+
+            $id = $1;
+            chomp $id;
+            $index -> {$id} = {'id_begin_position' => $id_begin_position, 'id_length' => length $line};
+            $logger->trace('Indexing sequence' . $id . ' (position_begin_id : '. $index -> {$id}{'id_begin_position'} . ', id_length : '. $index -> {$id}{'id_length'} .') from ' . $self->{file} . "\n");
+            <$fh>; <$fh>; <$fh>;
+        }
+
+        $id_begin_position = tell($fh);
+    }
+
+    $logger->info('File '.$self->{file}.' is now indexed (index contains '.(scalar keys %$index)." sequences)\n");
+    $self->{index} = $index;
+}
+
+=head2 loadFastqIndexFile
+
+=head2
+
+=head3 Description
+
+Retrieve index from file using Storable module
+
+=head3 Arguments
+
+=over 4
+
+An index file
+
+=back
+
+=head3 Returns
+
+=over 4
+
+=item
+
+A hash reference corresponding to the index of the input FASTQ file :
+
+$index -> {seq_id} = {'id_begin_position' => integer, 'id_length' => integer}
+
+=back
+
+=cut
+
+sub loadFastqIndexFile{
+
+	my ($self, $file) = @_;
+  $self->{index} = retrieve($file);
+  $logger->info('File '.$file." is now loaded\n");
+}
+
+=he=head2 writeFastaIndexFile
+
+=head2
+
+=head3 Description
+
+Write index to file using Storable module
+
+=head3 Arguments
+
+=over 4
+
+=item
+
+A hash reference corresponding to FASTQ index.
+
+=item
+
+An output file path where to store the index.
+
+=back
+
+=head3 Returns
+
+=over 4
+
+=item
+
+The output file path containing index
+
+=back
+
+=cut
+
+sub writeFastqIndexFile{
+	my ($self, $file) = @_;
+  $logger->info('Writing index ('.(scalar keys %{$self->{index}}).' sequences) in file : '.$file."\n");
+  store $self->{index}, $file;
+  $logger->info('File '.$file." is now created\n");
+}
+
+=head2 retrieveFastqSequence
+
+=head2
+
+=head3 Description
+
+Retrieve FASTQ sequences using a list of ids
+
+=head3 Arguments
+
+=over 4
+
+=item
+
+A sequence id OR an array reference containing the list of sequences id to retrieve.
+
+=back
+
+=head3 Returns
+
+=over 4
+
+=item
+
+A hash reference containing sequences id as keys and sequences as values
+
+$data -> {seq_id} = sequence_corresponding_to_seq_id
+
+=back
+
+=cut
+
+sub retrieveFastqSequence{
+	my ($self, $ids) = @_;
+	my $data={};
+  my $nbSequences = 0;
+  if(! ref $ids){$ids = [$ids]}
+  $logger->debug('Retrieving sequences of '.scalar(@$ids).' ids from indexed file : '.$self->{file}."\n");
+	my $fh = $self->{file_handle};
+	foreach my $id (@$ids){
+		my $cleanedId = $id;
+      if($id =~ /@(\S+)/){$cleanedId = $1}
+      $logger->trace('Retrieving informations of id ' . $cleanedId. " from index\n");
+      if(exists $self->{index} -> {$cleanedId}){
+        $logger->trace('id ' . $cleanedId . ' is present in index (id_begin_position : '. $self->{index} -> {$cleanedId}{'id_begin_position'}. ', id_length : '. $self->{index} -> {$cleanedId}{'id_length'}.")\n");
+        seek($fh, $self->{index} -> {$cleanedId}{'id_begin_position'}, 0);
+        <$fh>;
+        my $sequence = <$fh>;
+        $data->{$id} = $sequence;
+        $nbSequences ++;
+      	$logger->trace('Sequence of id '.$cleanedId.' is : ' . $sequence . "\n")
+    	}
+    	else{
+				$logger->trace('id ' . $cleanedId. " not found in index\n")
+			}
+	}
+  $logger->debug($nbSequences.'/'.scalar(@$ids).' sequences has been retrieved from indexed file ' . $self->{file} . "\n");
+	return $data;
+}
+
+=head2 retrieveFastqQuality
+
+=head2
+
+=head3 Description
+
+Retrieve FASTQ sequences quality using a list of ids
+
+=head3 Arguments
+
+=over 4
+
+=item
+
+A sequence id OR an array reference containing the list of sequences id to retrieve quality.
+
+=back
+
+=head3 Returns
+
+=over 4
+
+=item
+
+A hash reference containing sequences id as keys and sequences quality as values
+
+$data -> {seq_id} = sequence_quality_corresponding_to_seq_id
+
+=back
+
+=cut
+
+sub retrieveFastqQuality{
+	my ($self, $ids) = @_;
+	my $data;
+  my $nbSequences = 0;
+  if(! ref $ids){$ids = [$ids]}
+  $logger->debug('Retrieving sequence quality of '.scalar(@$ids).' ids from indexed file : '.$self->{file}."\n");
+	my $fh = $self->{file_handle};
+	foreach my $id (@$ids){
+		my $cleanedId = $id;
+		if($id =~ /@(\S+)/){
+			$cleanedId = $1;
+		}
+    $logger->trace('retrieving informations of id ' . $cleanedId. " from index\n");
+    if(exists $self->{index} -> {$cleanedId}){
+      $logger->trace('id ' . $cleanedId . ' is present in index (id_begin_position : '. $self->{index} -> {$cleanedId}{'id_begin_position'}. ', id_length : '. $self->{index} -> {$cleanedId}{'id_length'}.")\n");
+      seek($fh, $self->{index} -> {$cleanedId}{'id_begin_position'}, 0);
+      my $quality .= <$fh>.<$fh>.<$fh>;
+      $quality = <$fh>;
+      $data .= $quality;
+      $nbSequences ++;
+      $logger->trace('Sequence quality of id '.$cleanedId.' is : ' . $quality. "\n")
+    }
+    else{
+			$logger->trace('id ' . $cleanedId. " not found in index\n");
+		}
+	}
+  $logger->debug($nbSequences.'/'.scalar(@$ids).' sequences qualities has been retrieved from indexed file ' . $self->{file} . "\n");
+	return $data;
+}
+
+=head2 retrieveFastqBlock
+
+=head2
+
+=head3 Description
+
+Retrieve FASTQ formatted sequences using a list of ids
+
+=head3 Arguments
+
+=over 4
+
+=item
+
+A sequence id OR an array reference containing the list of sequences id to retrieve.
+
+=back
+
+=head3 Returns
+
+=over 4
+
+=item
+
+A scalar containing the sequences corresponding to ids in FASTQ format
+
+=back
+
+=cut
+
+sub retrieveFastqBlock{
+	my ($self, $ids) = @_;
+	my $data;
+  my $nbSequences = 0;
+
+  if(! ref $ids){$ids = [$ids]}
+
+  $logger->trace('Retrieving fastq block of '.scalar(@$ids).' ids from indexed file : '.$self->{file}."\n");
+	my $fh = $self->{file_handle};
+	foreach my $id (@$ids){
+		my $cleanedId = $id;
+		if($id =~ /@(\S+)/){
+			$cleanedId = $1;
+		}
+    $logger->trace('Retrieving informations of id ' . $cleanedId. " from index\n");
+    if(exists $self->{index} -> {$cleanedId}){
+      $logger->trace('id ' . $cleanedId . ' is present in index (id_begin_position : '. $self->{index} -> {$cleanedId}{'id_begin_position'}. ', id_length : '. $self->{index} -> {$cleanedId}{'id_length'}.")\n");
+      seek($fh, $self->{index} -> {$cleanedId}{'id_begin_position'}, 0);
+    	read($fh, my $block, $self->{index} -> {$cleanedId}{'id_length'});
+      $block .= <$fh>.<$fh>.<$fh>;
+      $data .= $block;
+      $nbSequences++;
+      $logger->trace('fastq block of id '.$cleanedId.' is : ' ."\n". $block. "\n")
+    }
+    else{
+			$logger->trace('id ' . $cleanedId. " not found in index\n");
+		}
+	}
+  $logger->trace($nbSequences.'/'.scalar(@$ids).' fastq block has been retrieved from indexed file ' . $self->{file} . "\n");
+	return $data;
+}
+1;

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/perl/scripts/readPerContig.pl	Thu Oct 15 09:53:48 2015 -0400
@@ -0,0 +1,179 @@
+#!/usr/bin/perl
+use strict;
+use Data::Dumper;
+use Logger::Logger;
+use File::Basename;
+use Getopt::Long;
+use Cwd 'abs_path' ;
+use Tools::Fasta ;
+use Tools::Fastq ;
+
+
+my $ref='';
+my @p1='';
+my @p2='';
+my @read='';
+my $identity = 95;
+my $coverage = 60;
+my $verbosity=1;
+my $format;
+my $stat;
+my $blatOutput='';
+my $statOutput='';
+
+GetOptions(
+	"r=s"              => \$ref,
+	"id=i"             => \$identity,
+	"cov=i"            => \$coverage,
+	"b|blat"	         => \$blatOutput,
+	"o|output=s"       =>	\$statOutput,
+	"f=s"		           => \$format,
+	"s=s"		           => \$stat,
+	"v|verbosity=i"    => \$verbosity
+);
+
+Logger::Logger->changeMode($verbosity);
+
+&main;
+
+sub main {
+	my $self = {};
+	bless $self;
+	$self->_setOptions();
+
+	$self->_checkFormat($format);
+
+	$self->{ref_tool} = Tools::Fasta->new(file => $self->{reference});
+
+	$self->_parseBlat();
+
+	$self->_print($self->{_statistics}, $self->{statOutput});
+}
+
+
+sub _parseBlat {
+	my ($self) = @_;
+	open(PSL,$self->{blatOutput}) || $logger->logdie('Cant read psl file ' . $self->{blatOutput});
+	while(<PSL>){
+		chomp;
+		my @line = split(/\t/,$_);
+		my $tSize = $line[14];
+		my $tStart = $line[15];
+		my $tEnd = $line[16];
+		my $coverage = (($tEnd-$tStart)/$tSize) * 100;
+
+		if($coverage >= $self->{_covThreshold}){
+			$self->{readNumber}->{$line[9]}++;
+			$self->{totalReadNumber}++;
+			$self->{size}->{$line[9]} = $line[10];
+			$self->{reads_size_sum}->{$line[9]} += $tSize;
+		}
+		else{
+			next;
+		}
+	}
+	close PSL;
+}
+
+
+sub _print {
+	my ($self, $mode, $statOutput) = @_;
+	$logger->info('Printing results ...');
+
+	if(!defined $mode){
+		$mode = 'nb_reads';
+	}
+
+	if(!defined $statOutput){
+		$statOutput = $self->{reference} . '.rn';
+	}
+
+	open(OUT,">$statOutput");
+	foreach my $ref (sort(keys(%{$self->{ref_tool}->{index}}))){
+		my $value = 0;
+		if(defined($self->{readNumber}->{$ref})){
+			if($mode eq 'nb_reads'){
+				$value = $self->{readNumber}->{$ref};
+			}
+			elsif($mode eq 'rpkm'){
+				$value = $self->{readNumber}->{$ref} / ($self->{size}->{$ref}/1000 * $self->{totalReadNumber}/1000000);
+			}
+			elsif($mode eq 'mean_coverage'){
+				$value =  $self->{reads_size_sum}->{$ref} / $self->{size}->{$ref};
+			}
+		}
+		print OUT $ref . "\t" . $value . "\n";
+	}
+	close OUT;
+}
+
+
+sub _setOptions {
+	my ($self) = @_;
+	if(-e $ref){
+		$self->{reference} = abs_path($ref);
+	}
+	else{
+		$logger->error('You must provide a reference.');
+		&help;
+	}
+	if($identity >= 0 && $identity <= 100){
+		$self->{_idThreshold} = $identity;
+	}
+	else{
+		$logger->logdie('ERROR: identity must be between 0 and 100.');
+	}
+	if($coverage >=0 && $coverage <= 100){
+		$self->{_covThreshold} = $coverage;
+	}
+	else{
+		$logger->logdie('ERROR: coverage must be between 0 and 100.');
+	}
+	if($stat =~ /nb_reads|rpkm|mean_coverage/){
+		$self->{_statistics} = $stat;
+	}
+	else{
+		$logdie('');
+	}
+	if($blatOutput eq ''){
+		$self->{blatOutput} = 'blat.psl';
+	}
+	else{
+		$self->{blatOutput} = $blatOutput;
+	}
+	if($statOutput eq ''){
+		my($filename, $dirs, $suffix) = fileparse($ref, qr/\.[^.]*/);
+		$statOutput = $filename . '.psl';
+	}
+	else{
+		$self->{statOutput} = $statOutput;
+	}
+}
+
+
+sub help {
+my $prog = basename($0) ;
+print STDERR <<EOF ;
+#### $prog ####
+#
+# AUTHOR:     Sebastien THEIL
+# LAST MODIF: 16/07/2015
+# PURPOSE:    This script is basically used to map reads (using blat) on contigs (or scaffolds) and count the
+              number of read per contig.
+              Input can be multiple fasta or fastq.
+              Output is a 2 column tabular file.
+
+USAGE:
+      $prog  -i singl.fastq -i singl.fasta -1 R1.fastq -2 R2.fastq ....
+
+      ### OPTIONS ###
+      -r          <string>   Rererence sequences file.
+      -id         <int>      Identity threshold. (Default: $identity)
+      -cov        <int>      Coverage threshold. (Default: $coverage)
+      -b          <string>   Blat output file path
+			-o          <string>   Output file path
+      -s          <string>   Statistics to print : nb_reads, rpkm or mean_coverage.
+      -v          <int>      Verbosity level. (0 -> 4).
+EOF
+exit(1);
+}

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/readPerContig.xml	Thu Oct 15 09:53:48 2015 -0400
@@ -0,0 +1,21 @@
+<tool id="readPerContig" name="readPerContig" version="1.0">
+	<description>
+	This script counts the number of read per contig using a Blat output.
+  Output is a 2 column tabular file.
+  </description>
+	<command interpreter="perl">readPerContig.pl-r $reference -id $identity -cov $coverage -b blat_result -v 0 -s $statistics	-o $output</command>
+	<inputs>
+		<param name="reference" type="data" format="fasta" label="References."/>
+		<param name="blat" type="data" format="psl" label="Blat .psl output file."/>
+		<param name="identity" type="integer" value="95" label="Identity threshold."/>
+		<param name="coverage" type="integer" value="60" label="Coverage threshold."/>
+		<param name="statistics" type="select" label="Statistics to print">
+			<option value="nb_reads">Read number</option>
+			<option value="rpkm">RPKM</option>
+			<option value="mean_coverage">Mean coverage</option>
+		</param>
+	</inputs>
+	<outputs>
+		<data name="output" format="tabular"/>
+	</outputs>
+</tool>

--- a/tool_dependencies.xml	Thu Oct 15 05:52:00 2015 -0400
+++ b/tool_dependencies.xml	Thu Oct 15 09:53:48 2015 -0400
@@ -11,12 +11,19 @@
             <package name="perl" version="5.18.1" />
           </repository>
         </action>
+        <action type="move_file">
+          <source>perl</source>
+          <destination>$INSTALL_DIR</destination>
+        </action>
         <action type="setup_perl_environment">
           <package>Data::Dumper</package>
           <package>File::Basename</package>
           <package>Getopt::Long</package>
           <package>Cwd</package>
-          <package>$REPOSITORY_INSTALL_DIR/perl/lib</package>
+          <package>$INSTALL_DIR/perl/lib</package>
+        </action>
+        <action type="set_environment">
+          <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/perl/scripts</environment_variable>
         </action>
       </actions>
     </install>