# HG changeset patch
# User simon-gladman
# Date 1405017533 14400
# Node ID cb56fdcbe0a5d2efdf40b5f5a960e4122d9d559d
# Parent  476184b9b2f73e670c22971a9af07c7d2dcd9be1
Uploaded

diff -r 476184b9b2f7 -r cb56fdcbe0a5 trimmomatic_wrapper.pl
--- a/trimmomatic_wrapper.pl	Thu Jul 10 14:38:25 2014 -0400
+++ b/trimmomatic_wrapper.pl	Thu Jul 10 14:38:53 2014 -0400
@@ -45,11 +45,11 @@
 
 my $cmd = "java -cp $jar org.usadellab.trimmomatic.Trimmomatic";
 
-if($stuff{"paired"} eq "True"){
-    $cmd .= "PE";
+if($stuff{"paired"} eq "single"){
+    $cmd .= "SE";
 }
 else {
-    $cmd .= "SE";
+    $cmd .= "PE";
 }
 
 $cmd .= " -threads $numthreads";
@@ -60,7 +60,7 @@
     $cmd .= " -trimlog " . $stuff{"logfile"};
 }
 
-if($stuff{"paired"} eq "True"){
+if($stuff{"paired"} ne "single"){
     $cmd .= " " . join(" ",($stuff{"fwdfile"},$stuff{"revfile"},$stuff{"fwdpairs"},$fwdtemp,$stuff{"revpairs"},$revtemp));
 }
 else {
@@ -84,7 +84,7 @@
 print "Command:\t$cmd\n";
 
 if(system($cmd) == 0){
-    if ($stuff{"paired"} eq "True"){
+    if ($stuff{"paired"} ne "single"){
         my $catcmd = "cat $fwdtemp $revtemp > " . $stuff{"singles"}; 
         system($catcmd) == 0 or die "Something went wrong with the cat command $!";
     }