# HG changeset patch
# User portiahollyoak
# Date 1461604541 14400
# Node ID 39cbc0965e077a00b362186b173d657bb09906a8
# Parent  28d1a6f8143f499b40b06a6079ae1fe70e771375
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty

diff -r 28d1a6f8143f -r 39cbc0965e07 temp.xml
--- a/temp.xml	Mon Apr 25 13:08:56 2016 -0400
+++ b/temp.xml	Mon Apr 25 13:15:41 2016 -0400
@@ -12,14 +12,14 @@
     </stdio>
     <command><![CDATA[
 
-        ln -f -s "${alignment.metadata.bam_index}" "${alignment.element_identifier}.bai" &&
-        ln -f -s "${alignment}" "${alignment.element_identifier}.bam" &&
-        bash $__tool_directory__/scripts/TEMP_Insertion.sh -i "$alignment" -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" -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 &&
-        mv ${alignment.element_identifier}.absence.refined.bp.summary $absence_summary &&
+        ln -f -s "$alignment.metadata.bam_index" "$alignment.element_identifier".bam.bai &&
+        ln -f -s "$alignment" "$alignment.element_identifier".bam &&
+        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 $insertion_bed &&
+        mv "$alignment.element_identifier".insertion.refined.bp $insertion_bed_refined &&
+        mv "$alignment.element_identifier".insertion.refined.bp.summary $insertion_summary &&
+        mv "$alignment.element_identifier".absence.refined.bp.summary $absence_summary &&
         zip $archive  *insertion* *excision* *absence*
     ]]></command>
     <inputs>