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comparison lumpy.xml @ 9:43462e6e9140 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 2d603534ddf6115d070e1459002fdb59931e5c15
author drosofff
date Mon, 12 Dec 2016 08:04:38 -0500
parents 382ffb8e0caa
children 4584440b2634
comparison
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8:382ffb8e0caa 9:43462e6e9140
1 <tool id="lumpy" name="lumpy-sv" version="0.2"> 1 <tool id="lumpy" name="lumpy-sv" version="0.2.1">
2 <description>find structural variants</description> 2 <description>find structural variants</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="0.2.12">lumpy-sv</requirement> 4 <requirement type="package" version="0.2.12">lumpy-sv</requirement>
5 <requirement type="package" version="1.3.1">samtools</requirement> 5 <requirement type="package" version="1.3.1">samtools</requirement>
6 <requirement type="package" version="1.11.2">numpy</requirement> 6 <requirement type="package" version="1.11.2">numpy</requirement>
23 samtools view -h input.bam | python $__tool_directory__/extractSplitReads_BwaMem.py -i stdin | samtools view -Sb - > "input.splitters.unsorted.bam" && 23 samtools view -h input.bam | python $__tool_directory__/extractSplitReads_BwaMem.py -i stdin | samtools view -Sb - > "input.splitters.unsorted.bam" &&
24 samtools sort input.discordants.unsorted.bam > input.discordants.bam && 24 samtools sort input.discordants.unsorted.bam > input.discordants.bam &&
25 samtools sort input.splitters.unsorted.bam > input.splitters.bam && 25 samtools sort input.splitters.unsorted.bam > input.splitters.bam &&
26 samtools view input.bam 26 samtools view input.bam
27 |tail -n +1 27 |tail -n +1
28 |python $__tool_directory__/pairend_distro.py -r $readLength -X 4 -N $seq_method.additional_params.samplingValue -o input.lib.histo > meandev.txt && 28 |python $__tool_directory__/pairend_distro.py -r $$analysis_type.readLength -X 4 -N $seq_method.additional_params.samplingValue -o input.lib.histo > meandev.txt &&
29 mean=\$(cat meandev.txt | sed s/mean:// | sed -r s/stdev:.+//) && 29 mean=\$(cat meandev.txt | sed s/mean:// | sed -r s/stdev:.+//) &&
30 stdev=\$(cat meandev.txt | sed -r s/mean:.+stdev://) && 30 stdev=\$(cat meandev.txt | sed -r s/mean:.+stdev://) &&
31 lumpy -mw $seq_method.additional_params.mw -tt $seq_method.additional_params.tt 31 lumpy -mw $seq_method.additional_params.mw -tt $seq_method.additional_params.tt
32 #if $output_format == "BEDPE": 32 #if $output_format == "BEDPE":
33 -b 33 -b
62 samtools sort input.B.discordants.unsorted.bam > input.B.discordants.bam && 62 samtools sort input.B.discordants.unsorted.bam > input.B.discordants.bam &&
63 samtools sort input.A.splitters.unsorted.bam > input.A.splitters.bam && 63 samtools sort input.A.splitters.unsorted.bam > input.A.splitters.bam &&
64 samtools sort input.B.splitters.unsorted.bam > input.B.splitters.bam && 64 samtools sort input.B.splitters.unsorted.bam > input.B.splitters.bam &&
65 samtools view input.A.bam 65 samtools view input.A.bam
66 |tail -n +1 66 |tail -n +1
67 |python $__tool_directory__/pairend_distro.py -r $readLength -X 4 -N $seq_method.additional_params.samplingValue -o input.A.lib.histo > meandevA.txt && 67 |python $__tool_directory__/pairend_distro.py -r $$analysis_type.readLength -X 4 -N $seq_method.additional_params.samplingValue -o input.A.lib.histo > meandevA.txt &&
68 samtools view input.B.bam 68 samtools view input.B.bam
69 |tail -n +1 69 |tail -n +1
70 |python $__tool_directory__/pairend_distro.py -r $readLengthB -X 4 -N $seq_method.additional_params.samplingValue -o input.B.lib.histo > meandevB.txt && 70 |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 &&
71 meanA=\$(cat meandevA.txt | sed s/mean:// | sed -r s/stdev:.+//) && 71 meanA=\$(cat meandevA.txt | sed s/mean:// | sed -r s/stdev:.+//) &&
72 meanB=\$(cat meandevB.txt | sed s/mean:// | sed -r s/stdev:.+//) && 72 meanB=\$(cat meandevB.txt | sed s/mean:// | sed -r s/stdev:.+//) &&
73 stdevA=\$(cat meandevA.txt | sed -r s/mean:.+stdev://) && 73 stdevA=\$(cat meandevA.txt | sed -r s/mean:.+stdev://) &&
74 stdevB=\$(cat meandevB.txt | sed -r s/mean:.+stdev://) && 74 stdevB=\$(cat meandevB.txt | sed -r s/mean:.+stdev://) &&
75 <<<<<<< HEAD 75 <<<<<<< HEAD