Previous changeset 9:43462e6e9140 (2016-12-12) Next changeset 11:ecbc563571ea (2016-12-12) |
Commit message:
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit a7bd16b6c6dbfe8b41de2a51c29b197ca660c5c6 |
modified:
lumpy.xml |
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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 |
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@@ -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://) && |