# HG changeset patch
# User portiahollyoak
# Date 1461771853 14400
# Node ID 3200a0299230896ad19c9466dbbfb88d4340daf0
# Parent 20a6e46295d67aa6be5f0b7076770ae4d557adb4
planemo upload for repository https://github.com/portiahollyoak/Tools commit debe4684eaa00ffcae3c79e7581fdbe41da91d5d
diff -r 20a6e46295d6 -r 3200a0299230 temp.xml
--- 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 @@
-
+
- samtools
+
+ bioperl
+ bwa
+ bedtools
+
perl-bioperl
bwa
bedtools
ucsc-twobittofa
+ samtools
@@ -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 @@
]]>
-
\ No newline at end of file
+
diff -r 20a6e46295d6 -r 3200a0299230 tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml Wed Apr 27 11:44:13 2016 -0400
@@ -0,0 +1,18 @@
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+