# HG changeset patch
# User portiahollyoak
# Date 1461608164 14400
# Node ID 2d566f713aeca98d262cd9f66eb9133b35ef25b2
# Parent  8c8cc2e2c0bc376761c6261d8de9b01e5c5a0a59
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty

diff -r 8c8cc2e2c0bc -r 2d566f713aec temp.xml
--- a/temp.xml	Mon Apr 25 14:13:34 2016 -0400
+++ b/temp.xml	Mon Apr 25 14:16:04 2016 -0400
@@ -12,8 +12,8 @@
     </stdio>
     <command><![CDATA[
 
-        ln -f -s "$alignment.metadata.bam_index" "$alignment.element_identifier".bam.bai &&
-        ln -f -s "$alignment" "$alignment.element_identifier".bam &&
+        ln -f -s "$alignment.metadata.bam_index" "$alignment.element_identifier".sorted.bam.bai &&
+        ln -f -s "$alignment" "$alignment.element_identifier".sorted.bam &&
         ls -l ;
         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} &&