# HG changeset patch
# User portiahollyoak
# Date 1461607686 14400
# Node ID 7c1d80867e88b3ec200d2a342c87b3f84d0b4816
# Parent  7ac983da5ad890930f1a06960b4616b4722be4e3
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty

diff -r 7ac983da5ad8 -r 7c1d80867e88 temp.xml
--- a/temp.xml	Mon Apr 25 13:24:46 2016 -0400
+++ b/temp.xml	Mon Apr 25 14:08:06 2016 -0400
@@ -1,10 +1,10 @@
 <tool id ="run_TEMP" name="Run TEMP" version=" 0.1.0">
     <description></description>
     <requirements>
+        <requirement type="package" version="0.1.19">samtools</requirement>
         <requirement type="package" version="1.6.924">perl-bioperl</requirement>
         <requirement type="package" version="0.7.13">bwa</requirement>
         <requirement type="package" version="2.25.0">bedtools</requirement>
-        <requirement type="package" version="0.1.19">samtools</requirement>
         <requirement type="package" version="324">ucsc-twobittofa</requirement>
     </requirements>
     <stdio>
@@ -14,8 +14,8 @@
 
         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} &&
+        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 "$reference2bit" -f 500 -c \${GALAXY_SLOTS:-2} &&
         mv "$alignment.element_identifier".insertion.bp.bed $insertion_bed &&
         mv "$alignment.element_identifier".insertion.refined.bp $insertion_bed_refined &&