Mercurial > repos > drosofff > lumpy

annotate lumpy.xml @ 2:b1e152172de9 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 commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
author drosofff
date Tue, 06 Dec 2016 17:29:34 -0500
parents a006d42dd759
children 0bd777f0d6d8
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
2
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
drosofff
parents: 1
diff changeset
1 <tool id="lumpy" name="lumpy-sv" version="0.2">
0
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
drosofff
parents:
diff changeset
2 <description>find structural variants</description>
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
drosofff
parents:
diff changeset
3 <requirements>
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
drosofff
parents:
diff changeset
4 <requirement type="package" version="0.2.12">lumpy-sv</requirement>
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
drosofff
parents:
diff changeset
5 <requirement type="package" version="1.3.1">samtools</requirement>
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
drosofff
parents:
diff changeset
6 <requirement type="package" version="1.11.2">numpy</requirement>
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
drosofff
parents:
diff changeset
7 </requirements>
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
drosofff
parents:
diff changeset
8 <stdio>
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
drosofff
parents:
diff changeset
9 <exit_code range="1:" level="fatal" description="Tool exception" />
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
drosofff
parents:
diff changeset
10 </stdio>
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
drosofff
parents:
diff changeset
11 <version_command>lumpy --version</version_command>
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
drosofff
parents:
diff changeset
12 <command><![CDATA[
2
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
drosofff
parents: 1
diff changeset
13 #if $analysis_type.analysis_type_list == "one_sample":
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
drosofff
parents: 1
diff changeset
14 ln -f -s $analysis_type.input_file input.bam &&
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
drosofff
parents: 1
diff changeset
15 #else:
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
drosofff
parents: 1
diff changeset
16 ln -f -s $analysis_type.input_file input.A.bam &&
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
drosofff
parents: 1
diff changeset
17 ln -f -s $analysis_type.input_fileB input.B.bam &&
0
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
drosofff
parents:
diff changeset
18 #end if
2
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
drosofff
parents: 1
diff changeset
19
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
drosofff
parents: 1
diff changeset
20 #if $analysis_type.analysis_type_list == "one_sample":
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
drosofff
parents: 1
diff changeset
21
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
drosofff
parents: 1
diff changeset
22 #if $seq_method.seq_method_list == "paired-end":
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
drosofff
parents: 1
diff changeset
23 samtools view -b -F 1294 input.bam > "input.discordants.unsorted.bam" &&
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
drosofff
parents: 1
diff changeset
24 samtools view -h input.bam | python $__tool_directory__/extractSplitReads_BwaMem.py -i stdin | samtools view -Sb - > "input.splitters.unsorted.bam" &&
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
drosofff
parents: 1
diff changeset
25 samtools sort input.discordants.unsorted.bam > input.discordants.bam &&
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
drosofff
parents: 1
diff changeset
26 samtools sort input.splitters.unsorted.bam > input.splitters.bam &&
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
drosofff
parents: 1
diff changeset
27 samtools view -r readgroup input.bam
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
drosofff
parents: 1
diff changeset
28 |tail -n +$seq_method.additional_params.samplingValue
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
drosofff
parents: 1
diff changeset
29 |python $__tool_directory__/pairend_distro.py -r 101 -X 4 -N $seq_method.additional_params.samplingValue -o input.lib.histo > meandev.txt &&
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
drosofff
parents: 1
diff changeset
30 mean=\$(cat meandev.txt | sed s/mean:// | sed -r s/stdev:.+//) &&
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
drosofff
parents: 1
diff changeset
31 stdev=\$(cat meandev.txt | sed -r s/mean:.+stdev://) &&
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
drosofff
parents: 1
diff changeset
32 lumpy -mw $seq_method.additional_params.mw -tt $seq_method.additional_params.tt
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
drosofff
parents: 1
diff changeset
33 -pe id:input.bam,bam_file:input.discordants.bam,histo_file:input.lib.histo,mean:"\$mean",stdev:"\$stdev",read_length:$seq_method.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:$seq_method.additional_params.min_mapping_threshold
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
drosofff
parents: 1
diff changeset
34 -sr id:input.bam,bam_file:input.splitters.bam,back_distance:$seq_method.additional_params.back_distance,weight:$seq_method.additional_params.weight,min_mapping_threshold:$seq_method.additional_params.min_mapping_threshold > output.vcf &&
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
drosofff
parents: 1
diff changeset
35 mv input.discordants.bam $discordants &&
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
drosofff
parents: 1
diff changeset
36 mv input.splitters.bam $splits &&
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
drosofff
parents: 1
diff changeset
37 mv input.lib.histo $histogram &&
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
drosofff
parents: 1
diff changeset
38 mv output.vcf $vcf_call &&
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
drosofff
parents: 1
diff changeset
39 rm input.discordants.unsorted.bam input.splitters.unsorted.bam meandev.txt
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
drosofff
parents: 1
diff changeset
40 #end if
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
drosofff
parents: 1
diff changeset
41 #if $seq_method.seq_method_list == "single-read":
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
drosofff
parents: 1
diff changeset
42 samtools view -h input.bam | python $__tool_directory__/extractSplitReads_BwaMem.py -i stdin | samtools view -Sb - > "input.splitters.unsorted.bam" &&
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
drosofff
parents: 1
diff changeset
43 lumpy -mw $seq_method.additional_params.mw -tt $seq_method.additional_params.tt
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
drosofff
parents: 1
diff changeset
44 -sr id:input.bam,bam_file:input.splitters.unsorted.bam,back_distance:$seq_method.additional_params.back_distance,weight:$seq_method.additional_params.weight,min_mapping_threshold:$seq_method.additional_params.min_mapping_threshold > output.vcf &&
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
drosofff
parents: 1
diff changeset
45 mv input.splitters.unsorted.bam $splits &&
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
drosofff
parents: 1
diff changeset
46 mv output.vcf $vcf_call
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
drosofff
parents: 1
diff changeset
47 #end if
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
drosofff
parents: 1
diff changeset
48
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
drosofff
parents: 1
diff changeset
49 #else:
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
drosofff
parents: 1
diff changeset
50
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
drosofff
parents: 1
diff changeset
51 #if $seq_method.seq_method_list == "paired-end":
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
drosofff
parents: 1
diff changeset
52 samtools view -b -F 1294 input.A.bam > "input.A.discordants.unsorted.bam" &&
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
drosofff
parents: 1
diff changeset
53 samtools view -b -F 1294 input.B.bam > "input.B.discordants.unsorted.bam" &&
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
drosofff
parents: 1
diff changeset
54 samtools view -h input.A.bam | python $__tool_directory__/extractSplitReads_BwaMem.py -i stdin | samtools view -Sb - > "input.A.splitters.unsorted.bam" &&
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
drosofff
parents: 1
diff changeset
55 samtools view -h input.B.bam | python $__tool_directory__/extractSplitReads_BwaMem.py -i stdin | samtools view -Sb - > "input.B.splitters.unsorted.bam" &&
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
drosofff
parents: 1
diff changeset
56 samtools sort input.A.discordants.unsorted.bam > input.A.discordants.bam &&
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
drosofff
parents: 1
diff changeset
57 samtools sort input.B.discordants.unsorted.bam > input.B.discordants.bam &&
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
drosofff
parents: 1
diff changeset
58 samtools sort input.A.splitters.unsorted.bam > input.A.splitters.bam &&
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
drosofff
parents: 1
diff changeset
59 samtools sort input.B.splitters.unsorted.bam > input.B.splitters.bam &&
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
drosofff
parents: 1
diff changeset
60 samtools view -r readgroup input.A.bam
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
drosofff
parents: 1
diff changeset
61 |tail -n +$seq_method.additional_params.samplingValue
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
drosofff
parents: 1
diff changeset
62 |python $__tool_directory__/pairend_distro.py -r 101 -X 4 -N $seq_method.additional_params.samplingValue -o input.A.lib.histo > meandevA.txt &&
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
drosofff
parents: 1
diff changeset
63 samtools view -r readgroup input.B.bam
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
drosofff
parents: 1
diff changeset
64 |tail -n +$seq_method.additional_params.samplingValue
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
drosofff
parents: 1
diff changeset
65 |python $__tool_directory__/pairend_distro.py -r 101 -X 4 -N $seq_method.additional_params.samplingValue -o input.B.lib.histo > meandevB.txt &&
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
drosofff
parents: 1
diff changeset
66 meanA=\$(cat meandevA.txt | sed s/mean:// | sed -r s/stdev:.+//) &&
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
drosofff
parents: 1
diff changeset
67 meanB=\$(cat meandevB.txt | sed s/mean:// | sed -r s/stdev:.+//) &&
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
drosofff
parents: 1
diff changeset
68 stdevA=\$(cat meandevA.txt | sed -r s/mean:.+stdev://) &&
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
drosofff
parents: 1
diff changeset
69 stdevB=\$(cat meandevB.txt | sed -r s/mean:.+stdev://) &&
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
drosofff
parents: 1
diff changeset
70 lumpy -mw $seq_method.additional_params.mw -tt $seq_method.additional_params.tt
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
drosofff
parents: 1
diff changeset
71 -pe id:inputA.bam,bam_file:input.A.discordants.bam,histo_file:input.A.lib.histo,mean:"\$meanA",stdev:"\$stdevA",read_length:$seq_method.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:$seq_method.additional_params.min_mapping_threshold
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
drosofff
parents: 1
diff changeset
72 -pe id:inputB.bam,bam_file:input.B.discordants.bam,histo_file:input.B.lib.histo,mean:"\$meanB",stdev:"\$stdevA",read_length:$seq_method.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:$seq_method.additional_params.min_mapping_threshold
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
drosofff
parents: 1
diff changeset
73 -sr id:inputA.bam,bam_file:input.A.splitters.bam,back_distance:$seq_method.additional_params.back_distance,weight:$seq_method.additional_params.weight,min_mapping_threshold:$seq_method.additional_params.min_mapping_threshold
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
drosofff
parents: 1
diff changeset
74 -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 > output.vcf &&
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
drosofff
parents: 1
diff changeset
75 mv input.A.discordants.bam $discordants &&
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
drosofff
parents: 1
diff changeset
76 mv input.B.discordants.bam $discordantsB &&
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
drosofff
parents: 1
diff changeset
77 mv input.A.splitters.bam $splits &&
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
drosofff
parents: 1
diff changeset
78 mv input.B.splitters.bam $splitsB &&
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
drosofff
parents: 1
diff changeset
79 mv input.A.lib.histo $histogram &&
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
drosofff
parents: 1
diff changeset
80 mv input.B.lib.histo $histogramB &&
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
drosofff
parents: 1
diff changeset
81 mv output.vcf $vcf_call &&
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
drosofff
parents: 1
diff changeset
82 rm input.A.discordants.unsorted.bam input.B.discordants.unsorted.bam input.A.splitters.unsorted.bam input.B.splitters.unsorted.bam meandevA.txt meandevB.txt
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
drosofff
parents: 1
diff changeset
83 #end if
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
drosofff
parents: 1
diff changeset
84 #if $seq_method.seq_method_list == "single-read":
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
drosofff
parents: 1
diff changeset
85 samtools view -h input.A.bam | python $__tool_directory__/extractSplitReads_BwaMem.py -i stdin | samtools view -Sb - > "input.A.splitters.unsorted.bam" &&
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
drosofff
parents: 1
diff changeset
86 samtools view -h input.B.bam | python $__tool_directory__/extractSplitReads_BwaMem.py -i stdin | samtools view -Sb - > "input.B.splitters.unsorted.bam" &&
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
drosofff
parents: 1
diff changeset
87 lumpy -mw $seq_method.additional_params.mw -tt $seq_method.additional_params.tt
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
drosofff
parents: 1
diff changeset
88 -sr id:input.A.bam,bam_file:input.A.splitters.unsorted.bam,back_distance:$seq_method.additional_params.back_distance,weight:$seq_method.additional_params.weight,min_mapping_threshold:$seq_method.additional_params.min_mapping_threshold
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
drosofff
parents: 1
diff changeset
89 -sr id:input.B.bam,bam_file:input.B.splitters.unsorted.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 > output.vcf &&
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
drosofff
parents: 1
diff changeset
90 mv input.A.splitters.unsorted.bam $splits &&
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
drosofff
parents: 1
diff changeset
91 mv input.B.splitters.unsorted.bam $splitsB &&
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
drosofff
parents: 1
diff changeset
92 mv output.vcf $vcf_call
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
drosofff
parents: 1
diff changeset
93 #end if
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
drosofff
parents: 1
diff changeset
94
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
drosofff
parents: 1
diff changeset
95
0
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
drosofff
parents:
diff changeset
96 #end if
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
drosofff
parents:
diff changeset
97
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
drosofff
parents:
diff changeset
98 ]]></command>
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
drosofff
parents:
diff changeset
99 <!-- basic error handling -->
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
drosofff
parents:
diff changeset
100 <inputs>
2
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
drosofff
parents: 1
diff changeset
101 <conditional name="analysis_type">
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
drosofff
parents: 1
diff changeset
102 <param help="Single or paired conditions (eg tumor vs normal)" label="Analysis type" name="analysis_type_list" type="select">
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
drosofff
parents: 1
diff changeset
103 <option selected="True" value="one_sample">One Sample</option>
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
drosofff
parents: 1
diff changeset
104 <option value="two_sample">Two samples</option>
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
drosofff
parents: 1
diff changeset
105 </param>
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
drosofff
parents: 1
diff changeset
106 <when value="one_sample">
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
drosofff
parents: 1
diff changeset
107 <param format="bam" name="input_file" type="data" label="One BAM alignment file produced by BWA-mem"/>
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
drosofff
parents: 1
diff changeset
108 </when>
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
drosofff
parents: 1
diff changeset
109 <when value="two_sample">
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
drosofff
parents: 1
diff changeset
110 <param format="bam" name="input_file" type="data" label="One BAM alignment file produced by BWA-mem"/>
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
drosofff
parents: 1
diff changeset
111 <param format="bam" name="input_fileB" type="data" label="One BAM alignment file produced by BWA-mem"/>
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
drosofff
parents: 1
diff changeset
112 </when>
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
drosofff
parents: 1
diff changeset
113 </conditional>
0
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
drosofff
parents:
diff changeset
114 <conditional name="seq_method">
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
drosofff
parents:
diff changeset
115 <param help="Paired-end or single-read sequencing" label="Sequencing method" name="seq_method_list" type="select">
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
drosofff
parents:
diff changeset
116 <option selected="True" value="paired-end">Paired-end sequencing</option>
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
drosofff
parents:
diff changeset
117 <option value="single-read">Single-read sequencing</option>
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
drosofff
parents:
diff changeset
118 </param>
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
drosofff
parents:
diff changeset
119 <when value="paired-end">
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
drosofff
parents:
diff changeset
120 <param name="readLength" value="151" type="integer" label="read length" help="e.g. 151 nt" />
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
drosofff
parents:
diff changeset
121 <section name="additional_params" title="Additional Options" expanded="False">
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
drosofff
parents:
diff changeset
122 <param name="samplingValue" value="100000" type="integer" label="number of reads to compute mean and stdev of read length" help="e.g. 10000" />
2
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
drosofff
parents: 1
diff changeset
123 <param name="mw" value="4" type="integer" label="-mw" help="minimum weight across all samples for a call (default: 4)" />
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
drosofff
parents: 1
diff changeset
124 <param name="tt" value="0" type="integer" label="-tt" help="trim threshold (default: 0)" />
0
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
drosofff
parents:
diff changeset
125 <param name="min_non_overlap" value="101" type="integer" label="min_non_overlap" help="e.g. 101" />
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
drosofff
parents:
diff changeset
126 <param name="discordant_z" value="5" type="integer" label="discordant_z" help="e.g. 5" />
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
drosofff
parents:
diff changeset
127 <param name="back_distance" value="10" type="integer" label="back_distance" help="e.g. 10" />
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
drosofff
parents:
diff changeset
128 <param name="weight" value="1" type="integer" label="weight" help="e.g. 1" />
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
drosofff
parents:
diff changeset
129 <param name="min_mapping_threshold" value="20" type="integer" label="min_mapping_threshold" help="e.g. 20" />
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
drosofff
parents:
diff changeset
130 </section>
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
drosofff
parents:
diff changeset
131 </when>
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
drosofff
parents:
diff changeset
132 <when value="single-read">
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
drosofff
parents:
diff changeset
133 <section name="additional_params" title="Additional Options" expanded="False">
2
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
drosofff
parents: 1
diff changeset
134 <param name="mw" value="4" type="integer" label="-mw" help="minimum weight across all samples for a call (default: 4)" />
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
drosofff
parents: 1
diff changeset
135 <param name="tt" value="0" type="integer" label="-tt" help="trim threshold (default: 0)" />
0
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
drosofff
parents:
diff changeset
136 <param name="back_distance" value="10" type="integer" label="back_distance" help="e.g. 10" />
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
drosofff
parents:
diff changeset
137 <param name="weight" value="1" type="integer" label="weight" help="e.g. 1" />
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
drosofff
parents:
diff changeset
138 <param name="min_mapping_threshold" value="20" type="integer" label="min_mapping_threshold" help="e.g. 20" />
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
drosofff
parents:
diff changeset
139 </section>
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
drosofff
parents:
diff changeset
140 </when>
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
drosofff
parents:
diff changeset
141
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
drosofff
parents:
diff changeset
142 </conditional>
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
drosofff
parents:
diff changeset
143
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
drosofff
parents:
diff changeset
144 </inputs>
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
drosofff
parents:
diff changeset
145
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
drosofff
parents:
diff changeset
146 <outputs>
2
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
drosofff
parents: 1
diff changeset
147 <data format="tabular" name="histogram" type="data" label="Lumpy on ${analysis_type.input_file.element_identifier}: Fragment size distribution">
0
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
drosofff
parents:
diff changeset
148 <filter>seq_method['seq_method_list'] == "paired-end"</filter>
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
drosofff
parents:
diff changeset
149 </data>
2
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
drosofff
parents: 1
diff changeset
150 <data format="tabular" name="histogramB" type="data" label="Lumpy on ${analysis_type.input_fileB.element_identifier}: Fragment size distribution">
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
drosofff
parents: 1
diff changeset
151 <filter>seq_method['seq_method_list'] == "paired-end"</filter>
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
drosofff
parents: 1
diff changeset
152 <filter>analysis_type['analysis_type_list'] == "two_sample"</filter>
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
drosofff
parents: 1
diff changeset
153 </data>
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
drosofff
parents: 1
diff changeset
154 <data format="bam" name="splits" type="data" label="Lumpy on ${analysis_type.input_file.element_identifier}: Split Reads (Bam format)"/>
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
drosofff
parents: 1
diff changeset
155 <data format="bam" name="splitsB" type="data" label="Lumpy on ${analysis_type.input_fileB.element_identifier}: Split Reads (Bam format)">
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
drosofff
parents: 1
diff changeset
156 <filter>analysis_type['analysis_type_list'] == "two_sample"</filter>
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
drosofff
parents: 1
diff changeset
157 </data>
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
drosofff
parents: 1
diff changeset
158 <data format="bam" name="discordants" type="data" label="Lumpy on ${analysis_type.input_file.element_identifier}: Discordant Pairs (Bam format)">
0
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
drosofff
parents:
diff changeset
159 <filter>seq_method['seq_method_list'] == "paired-end"</filter>
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
drosofff
parents:
diff changeset
160 </data>
2
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
drosofff
parents: 1
diff changeset
161 <data format="bam" name="discordantsB" type="data" label="Lumpy on ${analysis_type.input_fileB.element_identifier}: Discordant Pairs (Bam format)">
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
drosofff
parents: 1
diff changeset
162 <filter>seq_method['seq_method_list'] == "paired-end"</filter>
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
drosofff
parents: 1
diff changeset
163 <filter>analysis_type['analysis_type_list'] == "two_sample"</filter>
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
drosofff
parents: 1
diff changeset
164 </data>
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
drosofff
parents: 1
diff changeset
165 <data format="vcf" name="vcf_call" type="data" label="Lumpy Variant Calling (vcf format)"/>
0
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
drosofff
parents:
diff changeset
166 </outputs>
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
drosofff
parents:
diff changeset
167
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
drosofff
parents:
diff changeset
168 <tests>
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
drosofff
parents:
diff changeset
169 <test>
2
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
drosofff
parents: 1
diff changeset
170 <param name="analysis_type" value="one_sample" />
0
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
drosofff
parents:
diff changeset
171 <param name="input_file" value="sr.input.bam" ftype="bam"/>
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
drosofff
parents:
diff changeset
172 <param name="seq_method_list" value="single-read" />
2
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
drosofff
parents: 1
diff changeset
173 <param name="mw" value="4"/>
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
drosofff
parents: 1
diff changeset
174 <param name="tt" value="0"/>
0
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
drosofff
parents:
diff changeset
175 <param name="back_distance" value="10"/>
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
drosofff
parents:
diff changeset
176 <param name="weight" value="1" />
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
drosofff
parents:
diff changeset
177 <param name="min_mapping_threshold" value="20" />
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
drosofff
parents:
diff changeset
178 <output name="vcf_call" file="output.vcf" ftype="vcf"/>
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
drosofff
parents:
diff changeset
179 </test>
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
drosofff
parents:
diff changeset
180 </tests>
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
drosofff
parents:
diff changeset
181
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
drosofff
parents:
diff changeset
182 <help>
1
a006d42dd759 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit bd0a0b0717fd7da2ff703668b21ff7db3677d61b
drosofff
parents: 0
diff changeset
183
a006d42dd759 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit bd0a0b0717fd7da2ff703668b21ff7db3677d61b
drosofff
parents: 0
diff changeset
184 **lumpy-sv manual**
a006d42dd759 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit bd0a0b0717fd7da2ff703668b21ff7db3677d61b
drosofff
parents: 0
diff changeset
185
a006d42dd759 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit bd0a0b0717fd7da2ff703668b21ff7db3677d61b
drosofff
parents: 0
diff changeset
186 Read the lumpy-sv_ documentation for details on using lumpy.
a006d42dd759 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit bd0a0b0717fd7da2ff703668b21ff7db3677d61b
drosofff
parents: 0
diff changeset
187
a006d42dd759 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit bd0a0b0717fd7da2ff703668b21ff7db3677d61b
drosofff
parents: 0
diff changeset
188 .. _lumpy-sv: https://github.com/arq5x/lumpy-sv
a006d42dd759 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit bd0a0b0717fd7da2ff703668b21ff7db3677d61b
drosofff
parents: 0
diff changeset
189
a006d42dd759 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit bd0a0b0717fd7da2ff703668b21ff7db3677d61b
drosofff
parents: 0
diff changeset
190 **lumpy options**
a006d42dd759 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit bd0a0b0717fd7da2ff703668b21ff7db3677d61b
drosofff
parents: 0
diff changeset
191
a006d42dd759 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit bd0a0b0717fd7da2ff703668b21ff7db3677d61b
drosofff
parents: 0
diff changeset
192 v 0.2.13
a006d42dd759 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit bd0a0b0717fd7da2ff703668b21ff7db3677d61b
drosofff
parents: 0
diff changeset
193 Author: Ryan Layer (rl6sf@virginia.edu)
a006d42dd759 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit bd0a0b0717fd7da2ff703668b21ff7db3677d61b
drosofff
parents: 0
diff changeset
194
a006d42dd759 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit bd0a0b0717fd7da2ff703668b21ff7db3677d61b
drosofff
parents: 0
diff changeset
195 Summary: Find structural variations in various signals.
a006d42dd759 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit bd0a0b0717fd7da2ff703668b21ff7db3677d61b
drosofff
parents: 0
diff changeset
196
a006d42dd759 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit bd0a0b0717fd7da2ff703668b21ff7db3677d61b
drosofff
parents: 0
diff changeset
197 Options::
a006d42dd759 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit bd0a0b0717fd7da2ff703668b21ff7db3677d61b
drosofff
parents: 0
diff changeset
198
a006d42dd759 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit bd0a0b0717fd7da2ff703668b21ff7db3677d61b
drosofff
parents: 0
diff changeset
199 -g Genome file (defines chromosome order)
a006d42dd759 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit bd0a0b0717fd7da2ff703668b21ff7db3677d61b
drosofff
parents: 0
diff changeset
200 -e Show evidence for each call
a006d42dd759 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit bd0a0b0717fd7da2ff703668b21ff7db3677d61b
drosofff
parents: 0
diff changeset
201 -w File read windows size (default 1000000)
a006d42dd759 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit bd0a0b0717fd7da2ff703668b21ff7db3677d61b
drosofff
parents: 0
diff changeset
202 -mw minimum weight for a call
a006d42dd759 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit bd0a0b0717fd7da2ff703668b21ff7db3677d61b
drosofff
parents: 0
diff changeset
203 -msw minimum per-sample weight for a call
a006d42dd759 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit bd0a0b0717fd7da2ff703668b21ff7db3677d61b
drosofff
parents: 0
diff changeset
204 -tt trim threshold
a006d42dd759 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit bd0a0b0717fd7da2ff703668b21ff7db3677d61b
drosofff
parents: 0
diff changeset
205 -x exclude file bed file
a006d42dd759 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit bd0a0b0717fd7da2ff703668b21ff7db3677d61b
drosofff
parents: 0
diff changeset
206 -t temp file prefix, must be to a writeable directory
a006d42dd759 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit bd0a0b0717fd7da2ff703668b21ff7db3677d61b
drosofff
parents: 0
diff changeset
207 -P output probability curve for each variant
a006d42dd759 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit bd0a0b0717fd7da2ff703668b21ff7db3677d61b
drosofff
parents: 0
diff changeset
208 -b output BEDPE instead of VCF
a006d42dd759 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit bd0a0b0717fd7da2ff703668b21ff7db3677d61b
drosofff
parents: 0
diff changeset
209 -sr bam_file:&lt;file name&gt;,
a006d42dd759 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit bd0a0b0717fd7da2ff703668b21ff7db3677d61b
drosofff
parents: 0
diff changeset
210 id:&lt;sample name&gt;,
a006d42dd759 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit bd0a0b0717fd7da2ff703668b21ff7db3677d61b
drosofff
parents: 0
diff changeset
211 back_distance:&lt;distance&gt;,
a006d42dd759 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit bd0a0b0717fd7da2ff703668b21ff7db3677d61b
drosofff
parents: 0
diff changeset
212 min_mapping_threshold:&lt;mapping quality&gt;,
a006d42dd759 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit bd0a0b0717fd7da2ff703668b21ff7db3677d61b
drosofff
parents: 0
diff changeset
213 weight:&lt;sample weight&gt;,
a006d42dd759 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit bd0a0b0717fd7da2ff703668b21ff7db3677d61b
drosofff
parents: 0
diff changeset
214 min_clip:&lt;minimum clip length&gt;,
a006d42dd759 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit bd0a0b0717fd7da2ff703668b21ff7db3677d61b
drosofff
parents: 0
diff changeset
215 read_group:&lt;string&gt;
a006d42dd759 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit bd0a0b0717fd7da2ff703668b21ff7db3677d61b
drosofff
parents: 0
diff changeset
216
a006d42dd759 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit bd0a0b0717fd7da2ff703668b21ff7db3677d61b
drosofff
parents: 0
diff changeset
217 -pe bam_file:&lt;file name&gt;,
a006d42dd759 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit bd0a0b0717fd7da2ff703668b21ff7db3677d61b
drosofff
parents: 0
diff changeset
218 id:&lt;sample name&gt;,
a006d42dd759 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit bd0a0b0717fd7da2ff703668b21ff7db3677d61b
drosofff
parents: 0
diff changeset
219 histo_file:&lt;file name&gt;,
a006d42dd759 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit bd0a0b0717fd7da2ff703668b21ff7db3677d61b
drosofff
parents: 0
diff changeset
220 mean:&lt;value&gt;,
a006d42dd759 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit bd0a0b0717fd7da2ff703668b21ff7db3677d61b
drosofff
parents: 0
diff changeset
221 stdev:&lt;value&gt;,
a006d42dd759 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit bd0a0b0717fd7da2ff703668b21ff7db3677d61b
drosofff
parents: 0
diff changeset
222 read_length:&lt;length&gt;,
a006d42dd759 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit bd0a0b0717fd7da2ff703668b21ff7db3677d61b
drosofff
parents: 0
diff changeset
223 min_non_overlap:&lt;length&gt;,
a006d42dd759 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit bd0a0b0717fd7da2ff703668b21ff7db3677d61b
drosofff
parents: 0
diff changeset
224 discordant_z:&lt;z value&gt;,
a006d42dd759 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit bd0a0b0717fd7da2ff703668b21ff7db3677d61b
drosofff
parents: 0
diff changeset
225 back_distance:&lt;distance&gt;,
a006d42dd759 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit bd0a0b0717fd7da2ff703668b21ff7db3677d61b
drosofff
parents: 0
diff changeset
226 min_mapping_threshold:&lt;mapping quality&gt;,
a006d42dd759 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit bd0a0b0717fd7da2ff703668b21ff7db3677d61b
drosofff
parents: 0
diff changeset
227 weight:&lt;sample weight&gt;,
a006d42dd759 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit bd0a0b0717fd7da2ff703668b21ff7db3677d61b
drosofff
parents: 0
diff changeset
228 read_group:&lt;string&gt;
a006d42dd759 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit bd0a0b0717fd7da2ff703668b21ff7db3677d61b
drosofff
parents: 0
diff changeset
229
a006d42dd759 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit bd0a0b0717fd7da2ff703668b21ff7db3677d61b
drosofff
parents: 0
diff changeset
230 -bedpe bedpe_file:&lt;bedpe file&gt;,
a006d42dd759 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit bd0a0b0717fd7da2ff703668b21ff7db3677d61b
drosofff
parents: 0
diff changeset
231 id:&lt;sample name&gt;,
a006d42dd759 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit bd0a0b0717fd7da2ff703668b21ff7db3677d61b
drosofff
parents: 0
diff changeset
232 weight:&lt;sample weight&gt;
a006d42dd759 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit bd0a0b0717fd7da2ff703668b21ff7db3677d61b
drosofff
parents: 0
diff changeset
233
0
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
drosofff
parents:
diff changeset
234 </help>
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
drosofff
parents:
diff changeset
235
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
drosofff
parents:
diff changeset
236 <citations>
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
drosofff
parents:
diff changeset
237 <citation type="doi">10.1186/gb-2014-15-6-r84</citation>
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
drosofff
parents:
diff changeset
238 </citations>
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
drosofff
parents:
diff changeset
239 </tool>