# HG changeset patch
# User sarahinraauzeville
# Date 1513089048 18000
# Node ID 836946d90d26eb1328f43f9b2c7e2142fcb31b59
# Parent  fc7c00da3eeb844784b6b36f93226b011986c0f8
Uploaded perl file

diff -r fc7c00da3eeb -r 836946d90d26 sm_dos2unix.pl
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/sm_dos2unix.pl	Tue Dec 12 09:30:48 2017 -0500
@@ -0,0 +1,39 @@
+#!/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