# HG changeset patch
# User drosofff
# Date 1481550476 18000
# Node ID 4584440b2634e3c1b57eb93b5a24cbd827f91124
# Parent  43462e6e91403aed1b124fe8ceaad058d4d4bf99
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit a7bd16b6c6dbfe8b41de2a51c29b197ca660c5c6

diff -r 43462e6e9140 -r 4584440b2634 lumpy.xml
--- a/lumpy.xml	Mon Dec 12 08:04:38 2016 -0500
+++ b/lumpy.xml	Mon Dec 12 08:47:56 2016 -0500
@@ -25,7 +25,7 @@
                 samtools sort input.splitters.unsorted.bam > input.splitters.bam &&
                 samtools view input.bam
                     |tail -n +1
-                    |python $__tool_directory__/pairend_distro.py -r $$analysis_type.readLength -X 4 -N $seq_method.additional_params.samplingValue -o input.lib.histo > meandev.txt &&
+                    |python $__tool_directory__/pairend_distro.py -r $analysis_type.readLength -X 4 -N $seq_method.additional_params.samplingValue -o input.lib.histo > meandev.txt &&
                 mean=\$(cat meandev.txt | sed s/mean:// | sed -r s/stdev:.+//) &&
                 stdev=\$(cat meandev.txt | sed -r s/mean:.+stdev://) &&
                 lumpy -mw $seq_method.additional_params.mw -tt $seq_method.additional_params.tt
@@ -64,10 +64,10 @@
                 samtools sort input.B.splitters.unsorted.bam > input.B.splitters.bam &&
                 samtools view  input.A.bam
                     |tail -n +1
-                    |python $__tool_directory__/pairend_distro.py -r $$analysis_type.readLength -X 4 -N $seq_method.additional_params.samplingValue -o input.A.lib.histo > meandevA.txt &&
+                    |python $__tool_directory__/pairend_distro.py -r $analysis_type.readLength -X 4 -N $seq_method.additional_params.samplingValue -o input.A.lib.histo > meandevA.txt &&
                 samtools view  input.B.bam
                     |tail -n +1
-                    |python $__tool_directory__/pairend_distro.py -r $$analysis_type.readLengthB -X 4 -N $seq_method.additional_params.samplingValue -o input.B.lib.histo > meandevB.txt &&
+                    |python $__tool_directory__/pairend_distro.py -r $analysis_type.readLengthB -X 4 -N $seq_method.additional_params.samplingValue -o input.B.lib.histo > meandevB.txt &&
                 meanA=\$(cat meandevA.txt | sed s/mean:// | sed -r s/stdev:.+//) &&
                 meanB=\$(cat meandevB.txt | sed s/mean:// | sed -r s/stdev:.+//) &&
                 stdevA=\$(cat meandevA.txt | sed -r s/mean:.+stdev://) &&