# HG changeset patch
# User portiahollyoak
# Date 1461844632 14400
# Node ID e19d9742c99b0b9a6cad63a421970e6d5e2577ac
# Parent  3200a0299230896ad19c9466dbbfb88d4340daf0
planemo upload for repository https://github.com/portiahollyoak/Tools commit bfcc36291d97d1c0986f034ca1a03433e8299ff2-dirty

diff -r 3200a0299230 -r e19d9742c99b scripts/pickUniqPairFastq.pl
--- a/scripts/pickUniqPairFastq.pl	Wed Apr 27 11:44:13 2016 -0400
+++ b/scripts/pickUniqPairFastq.pl	Thu Apr 28 07:57:12 2016 -0400
@@ -21,7 +21,7 @@
 	## revcom the read mapped to the reverse strand
 	if($f[1]=~/r/)
 	{
-		my $seq=Bio::Seq->new(-seq=>$f[9]);
+		my $seq=Bio::Seq->new(-seq=>$f[9], -alphabet => 'dna');
 		$f[9]=$seq->revcom->seq;
 		$f[10]=reverse $f[10];
 	}
diff -r 3200a0299230 -r e19d9742c99b scripts/pickUniqPos.pl
--- a/scripts/pickUniqPos.pl	Wed Apr 27 11:44:13 2016 -0400
+++ b/scripts/pickUniqPos.pl	Thu Apr 28 07:57:12 2016 -0400
@@ -19,7 +19,7 @@
 	## revcomp
 	if($f[1]=~/r/)
         {
-                my $seq=Bio::Seq->new(-seq=>$f[9]);
+                my $seq=Bio::Seq->new(-seq=>$f[9], -alphabet => 'dna');
                 $f[9]=$seq->revcom->seq;
 		$strand="-";
         }
diff -r 3200a0299230 -r e19d9742c99b temp.xml
--- a/temp.xml	Wed Apr 27 11:44:13 2016 -0400
+++ b/temp.xml	Thu Apr 28 07:57:12 2016 -0400
@@ -20,7 +20,7 @@
 
         ln -f -s "$alignment.metadata.bam_index" alignment.sorted.bam.bai &&
         ln -f -s "$alignment" alignment.sorted.bam &&
-        bash $__tool_directory__/scripts/TEMP_Insertion.sh -i alignment.sorted.bam -s $__tool_directory__/scripts -r "$consensus_te_seqs" -t "$bed_te_locations" -m 3 -f "$median_insertsize" -c \${GALAXY_SLOTS:-2} &&
+        bash $__tool_directory__/scripts/TEMP_Insertion.sh -x 30 -i alignment.sorted.bam -s $__tool_directory__/scripts -r "$consensus_te_seqs" -t "$bed_te_locations" -m 3 -f "$median_insertsize" -c \${GALAXY_SLOTS:-2} &&
         bash $__tool_directory__/scripts/TEMP_Absence.sh -i alignment.sorted.bam -s $__tool_directory__/scripts -r "$bed_te_locations" -t "$reference2bit" -f 500 -c \${GALAXY_SLOTS:-2} &&
         mv alignment.insertion.bp.bed $insertion_bed &&
         mv alignment.insertion.refined.bp $insertion_bed_refined &&