# HG changeset patch
# User portiahollyoak
# Date 1461608014 14400
# Node ID 8c8cc2e2c0bc376761c6261d8de9b01e5c5a0a59
# Parent  7c1d80867e88b3ec200d2a342c87b3f84d0b4816
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty

diff -r 7c1d80867e88 -r 8c8cc2e2c0bc temp.xml
--- a/temp.xml	Mon Apr 25 14:08:06 2016 -0400
+++ b/temp.xml	Mon Apr 25 14:13:34 2016 -0400
@@ -15,8 +15,8 @@
         ln -f -s "$alignment.metadata.bam_index" "$alignment.element_identifier".bam.bai &&
         ln -f -s "$alignment" "$alignment.element_identifier".bam &&
         ls -l ;
-        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} && ls -l &&
-        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} &&
+        bash $__tool_directory__/scripts/TEMP_Insertion.sh -i "$alignment.element_identifier".sorted.bam -s $__tool_directory__/scripts -r "$consensus_te_seqs" -t "$bed_te_locations" -m 3 -f "$median_insertsize" -c \${GALAXY_SLOTS:-2} && ls -l &&
+        bash $__tool_directory__/scripts/TEMP_Absence.sh -i "$alignment.element_identifier".sorted.bam -s $__tool_directory__/scripts -r "$bed_te_locations" -t "$reference2bit" -f 500 -c \${GALAXY_SLOTS:-2} &&
         mv "$alignment.element_identifier".insertion.bp.bed $insertion_bed &&
         mv "$alignment.element_identifier".insertion.refined.bp $insertion_bed_refined &&
         mv "$alignment.element_identifier".insertion.refined.bp.summary $insertion_summary &&