changeset 2:7d626189cc4c draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/trimmomatic_wrapper.pl	Wed Jul 09 16:59:49 2014 -0400
@@ -0,0 +1,97 @@
+#!/usr/bin/perl
+
+#  trimmomatic_wrapper.pl
+#  
+#  Copyright 2012 Simon Gladman<[e-mail]>
+#  
+#  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 2 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, write to the Free Software
+#  Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+#  MA 02110-1301, USA.
+#  
+#  
+
+#Version 1.1 - goes with Trimmomatic-0.32.jar
+
+use strict;
+use warnings;
+use File::Temp qw( tempdir tempfile);
+
+my %stuff = @ARGV;
+
+my $dir = tempdir(CLEANUP => 1);
+my ($fwdtempfh, $fwdtemp) = tempfile( DIR => $dir );
+my ($revtempfh, $revtemp) = tempfile( DIR => $dir );
+
+foreach my $x (keys %stuff){
+    print "$x\t" . $stuff{$x} . "\n";
+}
+
+my $tooldir = $stuff{"tool-dir"};
+my $jar = "$tooldir/trimmomatic-0.32.jar";
+
+my $numthreads = $stuff{"threads"};
+
+
+my $cmd = "java -cp $jar org.usadellab.trimmomatic.Trimmomatic";
+
+if($stuff{"paired"} eq "True"){
+    $cmd .= "PE";
+}
+else {
+    $cmd .= "SE";
+}
+
+$cmd .= " -threads $numthreads";
+
+$cmd .= " -phred33" if($stuff{"phred"} eq "phred33");
+
+if($stuff{"log"} eq "True"){
+    $cmd .= " -trimlog " . $stuff{"logfile"};
+}
+
+if($stuff{"paired"} eq "True"){
+    $cmd .= " " . join(" ",($stuff{"fwdfile"},$stuff{"revfile"},$stuff{"fwdpairs"},$fwdtemp,$stuff{"revpairs"},$revtemp));
+}
+else {
+    $cmd .= " " . join(" ",($stuff{"fwdfile"},$stuff{"singles"}));
+}
+
+$cmd .= " " . join(":",("ILLUMINACLIP",$stuff{"adaptfile"},$stuff{"adaptseed"},$stuff{"adaptpalindrome"},$stuff{"adaptsimple"})) if $stuff{"cutadapt"} eq "True";
+
+$cmd .= " " . join(":",("SLIDINGWINDOW",$stuff{"slidingsize"},$stuff{"slidingqual"})) if $stuff{"slidingwindow"} eq "True";
+
+$cmd .= " " .join(":",("LEADING",$stuff{"leadingqual"})) if $stuff{"trimleading"} eq "True";
+
+$cmd .= " " .join(":",("TRAILING",$stuff{"trailingqual"})) if $stuff{"trimtrailing"} eq "True";
+
+$cmd .= " " .join(":",("CROP",$stuff{"croplen"})) if $stuff{"crop"} eq "True";
+
+$cmd .= " " .join(":",("HEADCROP",$stuff{"headcroplen"})) if $stuff{"headcrop"} eq "True";
+
+$cmd .= " " .join(":",("MINLEN",$stuff{"minlen"}));
+
+print "Command:\t$cmd\n";
+
+if(system($cmd) == 0){
+    if ($stuff{"paired"} eq "True"){
+        my $catcmd = "cat $fwdtemp $revtemp > " . $stuff{"singles"}; 
+        system($catcmd) == 0 or die "Something went wrong with the cat command $!";
+    }
+}
+else{
+    print "There was an error with trimmomatic! $!";
+    exit(1);
+}
+
+exit(0);