diff temp.xml @ 10:3200a0299230 draft

planemo upload for repository https://github.com/portiahollyoak/Tools commit debe4684eaa00ffcae3c79e7581fdbe41da91d5d

--- a/temp.xml	Tue Apr 26 06:36:46 2016 -0400
+++ b/temp.xml	Wed Apr 27 11:44:13 2016 -0400
@@ -1,11 +1,17 @@
-<tool id ="run_TEMP" name="Run TEMP" version=" 0.1.1">
+<tool id ="run_TEMP" name="Run TEMP" version=" 0.1.2">
     <description></description>
     <requirements>
-        <requirement type="package" version="0.1.19">samtools</requirement>
+        <!-- The following are classical toolshed packages and should be removed
+        once conda is deemed stable-->
+        <requirement type="package" version="1.6.922">bioperl</requirement>
+        <requirement type="package" version="0.7.12">bwa</requirement>
+        <requirement type="package" version="2.24">bedtools</requirement>
+        <!-- end of toolshed package definitions -->
         <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="324">ucsc-twobittofa</requirement>
+        <requirement type="package" version="0.1.19">samtools</requirement>
     </requirements>
     <stdio>
         <exit_code range="1:" />
@@ -14,7 +20,7 @@
 
         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_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} &&
         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 &&
@@ -67,4 +73,4 @@
 
 
     ]]> </help>
-</tool>
\ No newline at end of file
+</tool>