# HG changeset patch
# User portiahollyoak
# Date 1461666461 14400
# Node ID f60f60cf4a3454e2ca59697ec1839950b9494712
# Parent  e96a0d0f8dd6ff20594c0a2ad26ee292a359c978
planemo upload for repository https://github.com/portiahollyoak/Tools commit 2bc118a40da59fc3a2b8ee9ed04152c8effff94f

diff -r e96a0d0f8dd6 -r f60f60cf4a34 temp.xml
--- a/temp.xml	Mon Apr 25 14:20:48 2016 -0400
+++ b/temp.xml	Tue Apr 26 06:27:41 2016 -0400
@@ -1,4 +1,4 @@
-<tool id ="run_TEMP" name="Run TEMP" version=" 0.1.0">
+<tool id ="run_TEMP" name="Run TEMP" version=" 0.1.1">
     <description></description>
     <requirements>
         <requirement type="package" version="0.1.19">samtools</requirement>
@@ -12,15 +12,14 @@
     </stdio>
     <command><![CDATA[
 
-        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 "$reference2bit" -f 500 -c \${GALAXY_SLOTS:-2} &&
-        mv "$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.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} && ls -l &&
+        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 &&
+        mv alignment.insertion.refined.bp.summary $insertion_summary &&
+        mv alignment.absence.refined.bp.summary $absence_summary &&
         zip archive.zip  *insertion* *excision* *absence* &&
         mv archive.zip $archive
     ]]></command>