--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/sm_tophat2_toolshed.pl	Thu Feb 11 08:45:37 2016 -0500
@@ -0,0 +1,148 @@
+#!/usr/bin/perl -w
+
+# usage : perl sm_tophat.pl <read1 file> <read2 file>
+# Sarah Maman - 2016
+# Copyright (C) 2016 INRA
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+# 
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+#
+
+
+use strict;
+use File::Basename;
+use Config::IniFiles;
+
+my $cfg = Config::IniFiles->new( -file => "/path/to/PATH.ini" );
+my $path = $cfg->val( 'workPath', 'FILEPATH_DEV' );
+	
+my $TOPHAT = $cfg->val( 'toolsPath', 'TOPHAT2_PATH' );
+my $bowtie2build = $cfg->val( 'toolsPath', 'BOWTIE2_INDEXATION_PATH' );
+
+my $lib                     = $ARGV[0];
+my $input_read1             = $ARGV[1];
+my $input_read2             = $ARGV[2];
+my $reference_selector      = $ARGV[3];
+my $input_reference         = $ARGV[4];
+my $p                       = $ARGV[5];
+my $r                       = $ARGV[6];
+my $max_intron              = $ARGV[7];
+my $output_bam              = $ARGV[8];
+my $output_bed              = $ARGV[9];
+my $output_unmapped_bam     = $ARGV[10];
+my $zip                     = $ARGV[11];
+my $gtf_cond                = $ARGV[12];
+my $inputGTF                = $ARGV[13];
+
+
+print STDOUT "REFERENCE: *$input_reference*\n\n";
+
+my $cmd = ''; my $cmd2 = '';
+my $poption ="",
+my $roption ="";
+my $max_intron_option ="";
+my ($nb) = ($output_bam=~/galaxy_dataset_(\d+)\.\S+$/);
+my $liboption="";
+my $genome_index_base="";
+
+if (!$lib eq ""){$liboption = "--library-type $lib";}
+if (!$p eq ""){$poption = "-p $p";}
+if (!$r eq ""){$roption = "-r $r";}
+if (!$max_intron eq ""){$max_intron_option = "--max-intron-length $max_intron";}
+
+my $gtfoption ='';
+if (!$gtf_cond eq "F"){$gtfoption = "-G $inputGTF";}
+else {$gtfoption ="";}
+
+#Creation du repertoire de sortie des resultats
+`cd $path/; mkdir $nb/; chmod -R 777 $nb/;`;
+
+my $working_dir="$path/$nb/";
+# if the Biologist has his own reference file
+# generate the bowtie index for that reference
+print STDOUT "reference_selector : *$reference_selector*\n\n";
+if($reference_selector eq "history"){
+	
+	# copy your fasta file to the working directory
+	`cp $input_reference "$working_dir/reference.fasta"`;
+	chdir($working_dir) or die "system failed: chdir($working_dir) : $?"; 
+	my $info=`pwd`;
+	print STDOUT "INFO:Changed to working directory: $info \n ";
+	
+	# index the reference
+	# get the "genome_index_base" ?
+	$cmd = "($bowtie2build reference.fasta genome_index_base ) >& ./tophat.log 2>&1";
+	
+	#Info pour les biologistes
+	print STDOUT "Tophat : \n\n $cmd \n\n ";
+	system $cmd;
+	
+	# retrieve the new reference path
+	$genome_index_base="$path/$nb/genome_index_base";
+}
+else{
+	$genome_index_base=$input_reference;
+}
+
+print STDOUT "genome_index_base: *$genome_index_base*\n\n";
+
+#Donner l extension fastq.gz si les fichiers sont zippes
+if ($zip eq "YES"){
+	
+	print STDOUT "FASTQ files zipped ? $zip \n\n ";
+	`cp $input_read1 $input_read1.fastq.gz ; `;
+	`cp $input_read2 $input_read2.fastq.gz ; `;
+	
+	$cmd = "($TOPHAT -o '$path/$nb/' $poption $max_intron_option $roption $gtfoption $genome_index_base $input_read1.fastq.gz $input_read2.fastq.gz) >& ./tophat.log 2>&1";
+	
+	#Info pour les biologistes
+	print STDOUT "Tophat : \n\n $cmd \n\n ";
+	system $cmd;
+}
+else
+{
+	$cmd2 = "($TOPHAT -o '$path/$nb/' $liboption $poption $max_intron_option $roption $gtfoption $genome_index_base $input_read1 $input_read2) >& ./tophat.log 2>&1";
+	
+	#Info pour les biologistes
+	print STDOUT "Tophat : \n\n $cmd2 \n\n ";
+	system $cmd2;
+}
+
+
+
+if (! -e "$path/$nb/accepted_hits.bam")
+{
+print STDERR "BAM FILE NOT FOUND\n";
+}
+else
+{
+`mv "$path/$nb/accepted_hits.bam" $output_bam`;
+}
+
+if (! -e "$path/$nb/unmapped.bam")
+{
+print STDERR "unmapped.bam FILE NOT FOUND\n";
+}
+else
+{
+`mv "$path/$nb/unmapped.bam" $output_unmapped_bam`;
+}
+
+ 
+if (! -e "$path/$nb/junctions.bed")
+{
+print STDERR "JUNCTIONS BED FILE NOT FOUND\n";
+}
+else
+{
+`mv "$path/$nb/junctions.bed" $output_bed`;
+}