| Previous changeset 8:382ffb8e0caa (2016-12-10) Next changeset 10:4584440b2634 (2016-12-12) |
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Commit message:
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 2d603534ddf6115d070e1459002fdb59931e5c15 |
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modified:
lumpy.xml |
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| diff -r 382ffb8e0caa -r 43462e6e9140 lumpy.xml --- a/lumpy.xml Sat Dec 10 20:26:56 2016 -0500 +++ b/lumpy.xml Mon Dec 12 08:04:38 2016 -0500 |
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| @@ -1,4 +1,4 @@ -<tool id="lumpy" name="lumpy-sv" version="0.2"> +<tool id="lumpy" name="lumpy-sv" version="0.2.1"> <description>find structural variants</description> <requirements> <requirement type="package" version="0.2.12">lumpy-sv</requirement> @@ -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 $readLength -X 4 -N $seq_method.additional_params.samplingValue -o input.lib.histo > meandev.txt && + |python $__tool_directory__/pairend_distro.py -r $$analysis_type.readLength -X 4 -N $seq_method.additional_params.samplingValue -o input.lib.histo > meandev.txt && mean=\$(cat meandev.txt | sed s/mean:// | sed -r s/stdev:.+//) && stdev=\$(cat meandev.txt | sed -r s/mean:.+stdev://) && lumpy -mw $seq_method.additional_params.mw -tt $seq_method.additional_params.tt @@ -64,10 +64,10 @@ samtools sort input.B.splitters.unsorted.bam > input.B.splitters.bam && samtools view input.A.bam |tail -n +1 - |python $__tool_directory__/pairend_distro.py -r $readLength -X 4 -N $seq_method.additional_params.samplingValue -o input.A.lib.histo > meandevA.txt && + |python $__tool_directory__/pairend_distro.py -r $$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 $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://) && |