# HG changeset patch
# User portiahollyoak
# Date 1461605086 14400
# Node ID 7ac983da5ad890930f1a06960b4616b4722be4e3
# Parent  39cbc0965e077a00b362186b173d657bb09906a8
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty

diff -r 39cbc0965e07 -r 7ac983da5ad8 temp.xml
--- a/temp.xml	Mon Apr 25 13:15:41 2016 -0400
+++ b/temp.xml	Mon Apr 25 13:24:46 2016 -0400
@@ -14,6 +14,7 @@
 
         ln -f -s "$alignment.metadata.bam_index" "$alignment.element_identifier".bam.bai &&
         ln -f -s "$alignment" "$alignment.element_identifier".bam &&
+        samtools ;
         bash $__tool_directory__/scripts/TEMP_Insertion.sh -i "$alignment.element_identifier".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.element_identifier".bam -s $__tool_directory__/scripts -r "$bed_te_locations" -t "$reference2bit" -f 500 -c \${GALAXY_SLOTS:-2} &&
         mv "$alignment.element_identifier".insertion.bp.bed $insertion_bed &&