#!/usr/bin/perl -w

# usage : perl sm_FASTQ_qual.pl <file.fastq>
# 26/05/2015 
# Sarah Maman
# Copyright (C) 2014 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 Getopt::Long;
use lib "$ENV{'MY_GALAXY_DIR'}";
use GalaxyPath;


my $input1    = $ARGV[0];
my $output    = $ARGV[1];
my $cmd1      = ''; 

my $cfg = GalaxyPath->new( -file => $ENV{"GALAXY_CONFIG_FILE"} );
my $DOS = $cfg->my_path( 'toolsPath', 'DOS' );

$cmd1 = "($DOS -n $input1 $output) >& ./out_dos2unix.log 2>&1";
system $cmd1;
#Info pour les biologistes
print STDOUT "Command run on cluster : \n\n $cmd1 \n\n ";

#Recuperation des fichiers par Galaxy