Mercurial > repos > artbio > lumpy_sv

comparison lumpy.xml @ 2:6059f4cb4cf2 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy-sv commit 6a109f553d1691e243372258ad564244586875c3"
author artbio
date Mon, 14 Oct 2019 07:12:01 -0400
parents 1ed8619a5611
children da5aae7550b3
comparison
equal deleted inserted replaced
1:1ed8619a5611 2:6059f4cb4cf2
1 <tool id="lumpy" name="lumpy-sv" version="1.0.1"> 1 <tool id="lumpy" name="lumpy-sv" version="1.1.0">
2 <description>find structural variants</description> 2 <description>find structural variants</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="0.2.13">lumpy-sv</requirement> 4 <requirement type="package" version="0.2.13">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=py27_0">numpy</requirement> 6 <requirement type="package" version="1.11.2=py27_0">numpy</requirement>
25 #end if 25 #end if
26 26
27 #if $analysis_type.analysis_type_list == "one_sample": 27 #if $analysis_type.analysis_type_list == "one_sample":
28 28
29 #if $seq_method.seq_method_list == "paired-end": 29 #if $seq_method.seq_method_list == "paired-end":
30 samtools view -u -F 1294 '$one_sample_bam' | samtools sort -O bam -o input.discordants.bam && 30 samtools view -@ \${GALAXY_SLOTS:-4} -u -F 1294 '$one_sample_bam' | samtools sort -@ \${GALAXY_SLOTS:-4} -O bam -o input.discordants.bam &&
31 samtools view -h '$one_sample_bam' | python $__tool_directory__/extractSplitReads_BwaMem.py -i stdin | samtools sort -O bam -o input.splitters.bam && 31 samtools view -@ \${GALAXY_SLOTS:-4} -h '$one_sample_bam' | python $__tool_directory__/extractSplitReads_BwaMem.py -i stdin | samtools sort -@ \${GALAXY_SLOTS:-4} -O bam -o input.splitters.bam &&
32 samtools view '$one_sample_bam' 32 samtools view -@ \${GALAXY_SLOTS:-4} '$one_sample_bam'
33 |python $__tool_directory__/pairend_distro.py -r $analysis_type.readLength -X 4 -N $seq_method.additional_params.samplingValue -o input.lib.histo > meandev.txt && 33 |python $__tool_directory__/pairend_distro.py -r $analysis_type.readLength -X 4 -N $seq_method.additional_params.samplingValue -o input.lib.histo > meandev.txt &&
34 mean=\$(cat meandev.txt | sed s/mean:// | sed -r s/stdev:.+//) && 34 mean=\$(cat meandev.txt | sed s/mean:// | sed -r s/stdev:.+//) &&
35 stdev=\$(cat meandev.txt | sed -r s/mean:.+stdev://) && 35 stdev=\$(cat meandev.txt | sed -r s/mean:.+stdev://) &&
36 lumpy $seq_method.additional_params.evidence $seq_method.additional_params.probability_curve -mw $seq_method.additional_params.mw -tt $seq_method.additional_params.tt 36 lumpy $seq_method.additional_params.evidence $seq_method.additional_params.probability_curve -mw $seq_method.additional_params.mw -tt $seq_method.additional_params.tt
37 #if $output_format == "BEDPE": 37 #if $output_format == "BEDPE":
38 -b 38 -b
39 #end if 39 #end if
40 -pe id:'$one_sample_bam',bam_file:input.discordants.bam,histo_file:input.lib.histo,mean:"\$mean",stdev:"\$stdev",read_length:$analysis_type.readLength,min_non_overlap:$seq_method.additional_params.min_non_overlap,discordant_z:$seq_method.additional_params.discordant_z,back_distance:$seq_method.additional_params.back_distance,weight:$seq_method.additional_params.weight,min_mapping_threshold:$seq_method.additional_params.min_mapping_threshold 40 -pe id:'$one_sample_bam',bam_file:input.discordants.bam,histo_file:input.lib.histo,mean:"\$mean",stdev:"\$stdev",read_length:$analysis_type.readLength,min_non_overlap:$seq_method.additional_params.min_non_overlap,discordant_z:$seq_method.additional_params.discordant_z,back_distance:$seq_method.additional_params.back_distance,weight:$seq_method.additional_params.weight,min_mapping_threshold:$seq_method.additional_params.min_mapping_threshold
41 -sr id:'$one_sample_bam',bam_file:input.splitters.bam,back_distance:$seq_method.additional_params.back_distance,weight:$seq_method.additional_params.weight,min_mapping_threshold:$seq_method.additional_params.min_mapping_threshold > '$vcf_call' 41 -sr id:'$one_sample_bam',bam_file:input.splitters.bam,back_distance:$seq_method.additional_params.back_distance,weight:$seq_method.additional_params.weight,min_mapping_threshold:$seq_method.additional_params.min_mapping_threshold > '$vcf_call'
42 #elif $seq_method.seq_method_list == "single-read": 42 #elif $seq_method.seq_method_list == "single-read":
43 samtools view -h '$one_sample_bam' | python $__tool_directory__/extractSplitReads_BwaMem.py -i stdin | samtools sort -O bam -o input.splitters.bam && 43 samtools view -@ \${GALAXY_SLOTS:-4} -h '$one_sample_bam' | python $__tool_directory__/extractSplitReads_BwaMem.py -i stdin | samtools sort -@ \${GALAXY_SLOTS:-4} -O bam -o input.splitters.bam &&
44 lumpy $seq_method.additional_params.evidence $seq_method.additional_params.probability_curve -mw $seq_method.additional_params.mw -tt $seq_method.additional_params.tt 44 lumpy $seq_method.additional_params.evidence $seq_method.additional_params.probability_curve -mw $seq_method.additional_params.mw -tt $seq_method.additional_params.tt
45 #if $output_format == "BEDPE": 45 #if $output_format == "BEDPE":
46 -b 46 -b
47 #end if 47 #end if
48 -sr id:'$one_sample_bam',bam_file:input.splitters.bam,back_distance:$seq_method.additional_params.back_distance,weight:$seq_method.additional_params.weight,min_mapping_threshold:$seq_method.additional_params.min_mapping_threshold > '$vcf_call' 48 -sr id:'$one_sample_bam',bam_file:input.splitters.bam,back_distance:$seq_method.additional_params.back_distance,weight:$seq_method.additional_params.weight,min_mapping_threshold:$seq_method.additional_params.min_mapping_threshold > '$vcf_call'
49 #end if 49 #end if
50 #else: 50 #else:
51 #if $seq_method.seq_method_list == "paired-end": 51 #if $seq_method.seq_method_list == "paired-end":
52 samtools view -u -F 1294 '$sample_a_bam' | samtools sort -O bam -o input.discordants.bam && 52 samtools view -@ \${GALAXY_SLOTS:-4} -u -F 1294 '$sample_a_bam' | samtools sort -@ \${GALAXY_SLOTS:-4} -O bam -o input.discordants.bam &&
53 samtools view -u -F 1294 '$sample_b_bam' | samtools sort -O bam -o input.B.discordants.bam && 53 samtools view -@ \${GALAXY_SLOTS:-4} -u -F 1294 '$sample_b_bam' | samtools sort -@ \${GALAXY_SLOTS:-4} -O bam -o input.B.discordants.bam &&
54 samtools view -h '$sample_a_bam' | python $__tool_directory__/extractSplitReads_BwaMem.py -i stdin | samtools sort -O bam -o input.splitters.bam && 54 samtools view -@ \${GALAXY_SLOTS:-4} -h '$sample_a_bam' | python $__tool_directory__/extractSplitReads_BwaMem.py -i stdin | samtools sort -@ \${GALAXY_SLOTS:-4} -O bam -o input.splitters.bam &&
55 samtools view -h '$sample_b_bam' | python $__tool_directory__/extractSplitReads_BwaMem.py -i stdin | samtools sort -O bam -o input.B.splitters.bam && 55 samtools view -@ \${GALAXY_SLOTS:-4} -h '$sample_b_bam' | python $__tool_directory__/extractSplitReads_BwaMem.py -i stdin | samtools sort -@ \${GALAXY_SLOTS:-4} -O bam -o input.B.splitters.bam &&
56 samtools view '$sample_a_bam' 56 samtools view -@ \${GALAXY_SLOTS:-4} '$sample_a_bam'
57 |python $__tool_directory__/pairend_distro.py -r $analysis_type.readLength -X 4 -N $seq_method.additional_params.samplingValue -o input.lib.histo > meandevA.txt && 57 |python $__tool_directory__/pairend_distro.py -r $analysis_type.readLength -X 4 -N $seq_method.additional_params.samplingValue -o input.lib.histo > meandevA.txt &&
58 samtools view '$sample_b_bam' 58 samtools view -@ \${GALAXY_SLOTS:-4} '$sample_b_bam'
59 |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 && 59 |python $__tool_directory__/pairend_distro.py -r $analysis_type.readLengthB -X 4 -N $seq_method.additional_params.samplingValue -o input.B.lib.histo > meandevB.txt &&
60 meanA=\$(cat meandevA.txt | sed s/mean:// | sed -r s/stdev:.+//) && 60 meanA=\$(cat meandevA.txt | sed s/mean:// | sed -r s/stdev:.+//) &&
61 meanB=\$(cat meandevB.txt | sed s/mean:// | sed -r s/stdev:.+//) && 61 meanB=\$(cat meandevB.txt | sed s/mean:// | sed -r s/stdev:.+//) &&
62 stdevA=\$(cat meandevA.txt | sed -r s/mean:.+stdev://) && 62 stdevA=\$(cat meandevA.txt | sed -r s/mean:.+stdev://) &&
63 stdevB=\$(cat meandevB.txt | sed -r s/mean:.+stdev://) && 63 stdevB=\$(cat meandevB.txt | sed -r s/mean:.+stdev://) &&
68 -pe id:inputA.bam,bam_file:input.discordants.bam,histo_file:input.lib.histo,mean:"\$meanA",stdev:"\$stdevA",read_length:$analysis_type.readLength,min_non_overlap:$seq_method.additional_params.min_non_overlap,discordant_z:$seq_method.additional_params.discordant_z,back_distance:$seq_method.additional_params.back_distance,weight:$seq_method.additional_params.weight,min_mapping_threshold:$seq_method.additional_params.min_mapping_threshold 68 -pe id:inputA.bam,bam_file:input.discordants.bam,histo_file:input.lib.histo,mean:"\$meanA",stdev:"\$stdevA",read_length:$analysis_type.readLength,min_non_overlap:$seq_method.additional_params.min_non_overlap,discordant_z:$seq_method.additional_params.discordant_z,back_distance:$seq_method.additional_params.back_distance,weight:$seq_method.additional_params.weight,min_mapping_threshold:$seq_method.additional_params.min_mapping_threshold
69 -pe id:inputB.bam,bam_file:input.B.discordants.bam,histo_file:input.B.lib.histo,mean:"\$meanB",stdev:"\$stdevA",read_length:$analysis_type.readLengthB,min_non_overlap:$seq_method.additional_params.min_non_overlap,discordant_z:$seq_method.additional_params.discordant_z,back_distance:$seq_method.additional_params.back_distance,weight:$seq_method.additional_params.weight,min_mapping_threshold:$seq_method.additional_params.min_mapping_threshold 69 -pe id:inputB.bam,bam_file:input.B.discordants.bam,histo_file:input.B.lib.histo,mean:"\$meanB",stdev:"\$stdevA",read_length:$analysis_type.readLengthB,min_non_overlap:$seq_method.additional_params.min_non_overlap,discordant_z:$seq_method.additional_params.discordant_z,back_distance:$seq_method.additional_params.back_distance,weight:$seq_method.additional_params.weight,min_mapping_threshold:$seq_method.additional_params.min_mapping_threshold
70 -sr id:inputA.bam,bam_file:input.splitters.bam,back_distance:$seq_method.additional_params.back_distance,weight:$seq_method.additional_params.weight,min_mapping_threshold:$seq_method.additional_params.min_mapping_threshold 70 -sr id:inputA.bam,bam_file:input.splitters.bam,back_distance:$seq_method.additional_params.back_distance,weight:$seq_method.additional_params.weight,min_mapping_threshold:$seq_method.additional_params.min_mapping_threshold
71 -sr id:inputB.bam,bam_file:input.B.splitters.bam,back_distance:$seq_method.additional_params.back_distance,weight:$seq_method.additional_params.weight,min_mapping_threshold:$seq_method.additional_params.min_mapping_threshold > '$vcf_call' 71 -sr id:inputB.bam,bam_file:input.B.splitters.bam,back_distance:$seq_method.additional_params.back_distance,weight:$seq_method.additional_params.weight,min_mapping_threshold:$seq_method.additional_params.min_mapping_threshold > '$vcf_call'
72 #elif $seq_method.seq_method_list == "single-read": 72 #elif $seq_method.seq_method_list == "single-read":
73 samtools view -h '$sample_a_bam' | python $__tool_directory__/extractSplitReads_BwaMem.py -i stdin | samtools sort -O bam -o input.splitters.bam && 73 samtools view -@ \${GALAXY_SLOTS:-4} -h '$sample_a_bam' | python $__tool_directory__/extractSplitReads_BwaMem.py -i stdin | samtools sort -@ \${GALAXY_SLOTS:-4} -O bam -o input.splitters.bam &&
74 samtools view -h '$sample_b_bam' | python $__tool_directory__/extractSplitReads_BwaMem.py -i stdin | samtools sort -O bam -o input.B.splitters.bam && 74 samtools view -@ \${GALAXY_SLOTS:-4} -h '$sample_b_bam' | python $__tool_directory__/extractSplitReads_BwaMem.py -i stdin | samtools sort -@ \${GALAXY_SLOTS:-4} -O bam -o input.B.splitters.bam &&
75 lumpy $seq_method.additional_params.evidence $seq_method.additional_params.probability_curve -mw $seq_method.additional_params.mw -tt $seq_method.additional_params.tt 75 lumpy $seq_method.additional_params.evidence $seq_method.additional_params.probability_curve -mw $seq_method.additional_params.mw -tt $seq_method.additional_params.tt
76 #if $output_format == "BEDPE": 76 #if $output_format == "BEDPE":
77 -b 77 -b
78 #end if 78 #end if
79 -sr id:'$sample_a_bam',bam_file:input.splitters.bam,back_distance:$seq_method.additional_params.back_distance,weight:$seq_method.additional_params.weight,min_mapping_threshold:$seq_method.additional_params.min_mapping_threshold 79 -sr id:'$sample_a_bam',bam_file:input.splitters.bam,back_distance:$seq_method.additional_params.back_distance,weight:$seq_method.additional_params.weight,min_mapping_threshold:$seq_method.additional_params.min_mapping_threshold