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annotate lumpy.xml @ 12:b3fb23bbca8e draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 03ac2f3182f9e72db31297fa9e2fd5f0802343ea
author drosofff
date Sun, 18 Dec 2016 10:35:43 -0500
parents ecbc563571ea
children 02adb61c0246
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12
b3fb23bbca8e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 03ac2f3182f9e72db31297fa9e2fd5f0802343ea
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1 <tool id="lumpy" name="lumpy-sv" version="0.3.0">
0
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
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2 <description>find structural variants</description>
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
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3 <requirements>
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
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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
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5 <requirement type="package" version="1.3.1">samtools</requirement>
6
e9db5497e675 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit a4e9bbd84ef84934702f0c96aa04e7056d8ac235
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6 <requirement type="package" version="1.11.2">numpy</requirement>
0
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
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7 </requirements>
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
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8 <stdio>
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
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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
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10 </stdio>
5
745cbe841e40 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit ccfbe9e77653393089624d308873496d1d7e32a7
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11 <command detect_errors="exit_code"><![CDATA[
12
b3fb23bbca8e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 03ac2f3182f9e72db31297fa9e2fd5f0802343ea
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12 #import re
b3fb23bbca8e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 03ac2f3182f9e72db31297fa9e2fd5f0802343ea
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13 #set one_sample_bam = re.sub('[^\w\-]', '_', str($analysis_type.input_file.element_identifier))
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14 #if $analysis_type.analysis_type_list == "one_sample":
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b3fb23bbca8e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 03ac2f3182f9e72db31297fa9e2fd5f0802343ea
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15 ln -f -s '$analysis_type.input_file' '$one_sample_bam' &&
2
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
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16 #else:
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b3fb23bbca8e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 03ac2f3182f9e72db31297fa9e2fd5f0802343ea
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17 #set sample_a_bam = re.sub('[^\w\-]', '_', str($analysis_type.input_file.element_identifier))
b3fb23bbca8e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 03ac2f3182f9e72db31297fa9e2fd5f0802343ea
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18 #set sample_b_bam = re.sub('[^\w\-]', '_', str($analysis_type.input_fileB.element_identifier))
b3fb23bbca8e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 03ac2f3182f9e72db31297fa9e2fd5f0802343ea
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19 #if $sample_a_bam == $sample_b_bam:
b3fb23bbca8e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 03ac2f3182f9e72db31297fa9e2fd5f0802343ea
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20 #set sample_a_bam = "%s_a" % str($sample_a_bam)
b3fb23bbca8e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 03ac2f3182f9e72db31297fa9e2fd5f0802343ea
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21 #set sample_b_bam = "%s_b" % str($sample_b_bam)
b3fb23bbca8e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 03ac2f3182f9e72db31297fa9e2fd5f0802343ea
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22 #end if
b3fb23bbca8e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 03ac2f3182f9e72db31297fa9e2fd5f0802343ea
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23 ln -f -s '$analysis_type.input_file' '$sample_a_bam' &&
b3fb23bbca8e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 03ac2f3182f9e72db31297fa9e2fd5f0802343ea
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24 ln -f -s '$analysis_type.input_fileB' '$sample_b_bam' &&
0
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
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25 #end if
2
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b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
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27 #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
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28
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
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29 #if $seq_method.seq_method_list == "paired-end":
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b3fb23bbca8e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 03ac2f3182f9e72db31297fa9e2fd5f0802343ea
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30 samtools view -u -F 1294 '$one_sample_bam' | samtools sort -O bam -o input.discordants.bam &&
b3fb23bbca8e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 03ac2f3182f9e72db31297fa9e2fd5f0802343ea
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31 samtools view -h '$one_sample_bam' | python $__tool_directory__/extractSplitReads_BwaMem.py -i stdin | samtools sort -O bam -o input.splitters.bam &&
b3fb23bbca8e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 03ac2f3182f9e72db31297fa9e2fd5f0802343ea
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32 samtools view '$one_sample_bam'
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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 &&
2
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
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34 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
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35 stdev=\$(cat meandev.txt | sed -r s/mean:.+stdev://) &&
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b3fb23bbca8e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 03ac2f3182f9e72db31297fa9e2fd5f0802343ea
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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
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e833b178b94b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 834a0ca8b5cc29307a03c1b22a372152ed064abd
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37 #if $output_format == "BEDPE":
e833b178b94b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 834a0ca8b5cc29307a03c1b22a372152ed064abd
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38 -b
e833b178b94b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 834a0ca8b5cc29307a03c1b22a372152ed064abd
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39 #end if
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b3fb23bbca8e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 03ac2f3182f9e72db31297fa9e2fd5f0802343ea
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40 -pe id:'$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
b3fb23bbca8e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 03ac2f3182f9e72db31297fa9e2fd5f0802343ea
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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'
b3fb23bbca8e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 03ac2f3182f9e72db31297fa9e2fd5f0802343ea
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42 #elif $seq_method.seq_method_list == "single-read":
b3fb23bbca8e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 03ac2f3182f9e72db31297fa9e2fd5f0802343ea
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43 samtools view -h '$one_sample_bam' | python $__tool_directory__/extractSplitReads_BwaMem.py -i stdin | samtools sort -O bam -o input.splitters.bam &&
b3fb23bbca8e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 03ac2f3182f9e72db31297fa9e2fd5f0802343ea
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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
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45 #if $output_format == "BEDPE":
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46 -b
e833b178b94b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 834a0ca8b5cc29307a03c1b22a372152ed064abd
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47 #end if
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48 -sr id:'$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'
2
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
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49 #end if
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
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50 #else:
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
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51 #if $seq_method.seq_method_list == "paired-end":
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52 samtools view -u -F 1294 '$sample_a_bam' | samtools sort -O bam -o input.discordants.bam &&
b3fb23bbca8e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 03ac2f3182f9e72db31297fa9e2fd5f0802343ea
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53 samtools view -u -F 1294 '$sample_b_bam' | samtools sort -O bam -o input.B.discordants.bam &&
b3fb23bbca8e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 03ac2f3182f9e72db31297fa9e2fd5f0802343ea
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54 samtools view -h '$sample_a_bam' | python $__tool_directory__/extractSplitReads_BwaMem.py -i stdin | samtools sort -O bam -o input.splitters.bam &&
b3fb23bbca8e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 03ac2f3182f9e72db31297fa9e2fd5f0802343ea
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55 samtools view -h '$sample_b_bam' | python $__tool_directory__/extractSplitReads_BwaMem.py -i stdin | samtools sort -O bam -o input.B.splitters.bam &&
b3fb23bbca8e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 03ac2f3182f9e72db31297fa9e2fd5f0802343ea
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56 samtools view '$sample_a_bam'
b3fb23bbca8e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 03ac2f3182f9e72db31297fa9e2fd5f0802343ea
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57 |python $__tool_directory__/pairend_distro.py -r $analysis_type.readLength -X 4 -N $seq_method.additional_params.samplingValue -o input.lib.histo > meandevA.txt &&
b3fb23bbca8e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 03ac2f3182f9e72db31297fa9e2fd5f0802343ea
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58 samtools view '$sample_b_bam'
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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 &&
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60 meanA=\$(cat meandevA.txt | sed s/mean:// | sed -r s/stdev:.+//) &&
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61 meanB=\$(cat meandevB.txt | sed s/mean:// | sed -r s/stdev:.+//) &&
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62 stdevA=\$(cat meandevA.txt | sed -r s/mean:.+stdev://) &&
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63 stdevB=\$(cat meandevB.txt | sed -r s/mean:.+stdev://) &&
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64 lumpy $seq_method.additional_params.evidence $seq_method.additional_params.probability_curve -mw $seq_method.additional_params.mw -tt $seq_method.additional_params.tt
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65 #if $output_format == "BEDPE":
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66 -b
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67 #end if
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68 -pe id:inputA.bam,bam_file:input.discordants.bam,histo_file:input.lib.histo,mean:"\$meanA",stdev:"\$stdevA",read_length:$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:$seq_method.additional_params.min_mapping_threshold
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382ffb8e0caa planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 8375ddf784506b68d28bc9e6224648fafa796d9f
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69 -pe id:inputB.bam,bam_file:input.B.discordants.bam,histo_file:input.B.lib.histo,mean:"\$meanB",stdev:"\$stdevA",read_length:$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:$seq_method.additional_params.min_mapping_threshold
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b3fb23bbca8e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 03ac2f3182f9e72db31297fa9e2fd5f0802343ea
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70 -sr id:inputA.bam,bam_file:input.splitters.bam,back_distance:$seq_method.additional_params.back_distance,weight:$seq_method.additional_params.weight,min_mapping_threshold:$seq_method.additional_params.min_mapping_threshold
b3fb23bbca8e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 03ac2f3182f9e72db31297fa9e2fd5f0802343ea
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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'
b3fb23bbca8e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 03ac2f3182f9e72db31297fa9e2fd5f0802343ea
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72 #elif $seq_method.seq_method_list == "single-read":
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73 samtools view -h '$sample_a_bam' | python $__tool_directory__/extractSplitReads_BwaMem.py -i stdin | samtools sort -O bam -o input.splitters.bam &&
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74 samtools view -h '$sample_b_bam' | python $__tool_directory__/extractSplitReads_BwaMem.py -i stdin | samtools sort -O bam -o input.B.splitters.bam &&
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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
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76 #if $output_format == "BEDPE":
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77 -b
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78 #end if
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79 -sr id:'$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:$seq_method.additional_params.min_mapping_threshold
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80 -sr id:'$sample_b_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'
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81 #end if
0
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82 #end if
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83
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84 ]]></command>
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85 <!-- basic error handling -->
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86 <inputs>
2
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87 <conditional name="analysis_type">
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88 <param help="Single or paired conditions (eg tumor vs normal)" label="Input(s)" name="analysis_type_list" type="select">
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89 <option selected="True" value="one_sample">One Sample</option>
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90 <option value="two_sample">Two samples</option>
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91 </param>
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92 <when value="one_sample">
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93 <param format="bam" name="input_file" type="data" label="One BAM alignment file produced by BWA-mem"/>
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94 <param name="readLength" value="151" type="integer" label="read length" help="e.g. 151 nt" />
2
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95 </when>
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96 <when value="two_sample">
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97 <param format="bam" name="input_file" type="data" label="One BAM alignment file produced by BWA-mem"/>
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98 <param name="readLength" value="151" type="integer" label="read length" help="e.g. 151 nt" />
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99 <param format="bam" name="input_fileB" type="data" label="One BAM alignment file produced by BWA-mem"/>
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100 <param name="readLengthB" value="151" type="integer" label="read length" help="e.g. 151 nt" />
2
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101 </when>
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102 </conditional>
0
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103 <conditional name="seq_method">
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104 <param help="Paired-end or single-read sequencing" label="Sequencing method" name="seq_method_list" type="select">
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105 <option selected="True" value="paired-end">Paired-end sequencing</option>
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106 <option value="single-read">Single-read sequencing</option>
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107 </param>
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108 <when value="paired-end">
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109 <section name="additional_params" title="Additional Options" expanded="False">
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110 <param name="samplingValue" value="100000" type="integer" label="number of reads to compute mean and stdev of read length" help="e.g. 10000" />
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111 <param name="mw" value="4" type="integer" label="-mw" help="minimum weight across all samples for a call (default: 4)" />
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112 <param name="tt" value="0" type="integer" label="-tt" help="trim threshold (default: 0)" />
0
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113 <param name="min_non_overlap" value="101" type="integer" label="min_non_overlap" help="e.g. 101" />
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114 <param name="discordant_z" value="5" type="integer" label="discordant_z" help="e.g. 5" />
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115 <param name="back_distance" value="10" type="integer" label="back_distance" help="e.g. 10" />
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116 <param name="weight" value="1" type="integer" label="weight" help="e.g. 1" />
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117 <param name="min_mapping_threshold" value="20" type="integer" label="min_mapping_threshold" help="e.g. 20" />
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118 <param name="probability_curve" argument="-P" type="boolean" truevalue="-P" falsevalue="" checked="true" label="output probability curve for each variant"/>
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119 <param name="evidence" argument="-e" type="boolean" truevalue="-e" falsevalue="" checked="true" label="show evidence for each call"/>
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120 </section>
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121 </when>
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122 <when value="single-read">
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123 <section name="additional_params" title="Additional Options" expanded="False">
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124 <param name="mw" value="4" type="integer" label="-mw" help="minimum weight across all samples for a call (default: 4)" />
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125 <param name="tt" value="0" type="integer" label="-tt" help="trim threshold (default: 0)" />
0
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126 <param name="back_distance" value="10" type="integer" label="back_distance" help="e.g. 10" />
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127 <param name="weight" value="1" type="integer" label="weight" help="e.g. 1" />
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128 <param name="min_mapping_threshold" value="20" type="integer" label="min_mapping_threshold" help="e.g. 20" />
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129 <param name="probability_curve" argument="-P" type="boolean" truevalue="-P" falsevalue="" checked="false" label="output probability curve for each variant"/>
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130 <param name="evidence" argument="-e" type="boolean" truevalue="-e" falsevalue="" checked="false" label="show evidence for each call"/>
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131 </section>
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132 </when>
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133
0
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134 </conditional>
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135 <param help="get variant calling in vcf or BEDPE format" label="variant calling format" name="output_format" type="select">
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136 <option selected="True" value="vcf">vcf</option>
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137 <option value="BEDPE">BEDPE</option>
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138 </param>
0
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139 </inputs>
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140
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141 <outputs>
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142 <data format="tabular" name="histogram" label="Lumpy on ${on_string}: Fragment size distribution" from_work_dir="input.lib.histo">
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143 <filter>seq_method['seq_method_list'] == "paired-end"</filter>
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144 </data>
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145 <data format="tabular" name="histogramB" label="Lumpy on ${on_string}: Fragment size distribution" from_work_dir="input.B.lib.histo">
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146 <filter>seq_method['seq_method_list'] == "paired-end"</filter>
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147 <filter>analysis_type['analysis_type_list'] == "two_sample"</filter>
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148 </data>
12
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149 <data format="bam" name="splits" label="Lumpy on ${on_string}: Split Reads (Bam format)" from_work_dir="input.splitters.bam"/>
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150 <data format="bam" name="splitsB" label="Lumpy on ${on_string}: Split Reads (Bam format)" from_work_dir="input.B.splitters.bam">
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151 <filter>analysis_type['analysis_type_list'] == "two_sample"</filter>
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152 </data>
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153 <data format="bam" name="discordants" label="Lumpy on ${on_string}: Discordant Pairs (Bam format)" from_work_dir="input.discordants.bam">
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154 <filter>seq_method['seq_method_list'] == "paired-end"</filter>
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155 </data>
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156 <data format="bam" name="discordantsB" label="Lumpy on ${on_string}: Discordant Pairs (Bam format)" from_work_dir="input.discordants.B.bam">
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157 <filter>seq_method['seq_method_list'] == "paired-end"</filter>
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158 <filter>analysis_type['analysis_type_list'] == "two_sample"</filter>
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159 </data>
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160 <data format="vcf" name="vcf_call" label="Lumpy Variant Calling">
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161 <change_format>
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162 <when format="tabular" input="output_format" value="BEDPE" />
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163 </change_format>
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164 </data>
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165 </outputs>
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166
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167 <tests>
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168 <test>
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169 <param name="analysis_type_list" value="one_sample" />
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170 <param name="input_file" value="sr.input.bam" ftype="bam"/>
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171 <param name="seq_method_list" value="single-read" />
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172 <param name="mw" value="4"/>
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173 <param name="tt" value="0"/>
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174 <param name="back_distance" value="10"/>
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175 <param name="weight" value="1" />
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176 <param name="min_mapping_threshold" value="20" />
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177 <output name="vcf_call" file="output.vcf" ftype="vcf"/>
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178 </test>
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179 <test>
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180 <param name="analysis_type_list" value="one_sample" />
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181 <param name="input_file" value="sr.input.bam" ftype="bam"/>
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182 <param name="seq_method_list" value="single-read" />
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183 <param name="mw" value="4"/>
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184 <param name="tt" value="0"/>
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185 <param name="back_distance" value="10"/>
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186 <param name="weight" value="1" />
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187 <param name="min_mapping_threshold" value="20" />
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188 <param name="evidence" value="true" />
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189 <param name="probability_curve" value="true" />
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190 <output name="vcf_call" file="output_extended.vcf" ftype="vcf" compare="sim_size"/>
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191 </test>
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192 <test>
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193 <param name="analysis_type_list" value="two_sample" />
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194 <param name="input_file" value="sr.input.bam" ftype="bam"/>
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195 <param name="input_fileB" value="sr.input.bam" ftype="bam"/>
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196 <param name="seq_method_list" value="single-read" />
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197 <param name="mw" value="4"/>
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198 <param name="tt" value="0"/>
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199 <param name="back_distance" value="10"/>
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200 <param name="weight" value="1" />
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201 <param name="min_mapping_threshold" value="20" />
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202 <output name="vcf_call" file="output_two.vcf" ftype="vcf"/>
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203 </test>
0
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204 </tests>
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205
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206 <help>
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207
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208 **Input(s)**
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209
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210 *One sample* : lumpy search structural variations inside a single sequencing dataset
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211
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212 *Two samples*: lumpy search structural variations inside and across two sequencing datasets from two samples
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213
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214 Analysis of sample replicates is not implemented yet in this wrapper
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215
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216 *BAM files*: Only BAM alignments produced by BWA-mem have been tested with this tool
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217
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218 **Sequencing method**
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219
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220 *Paired-end sequencing*: Both ends of library fragments have been sequenced, resulting in two paired sequencing datasets
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221
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222 *Single-read sequencing*: Only one end of library fragment has been sequenced, resulting in a single sequencing dataset. Under these conditions, evidences of structural variation are obtained only from splited read alignments
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223
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224 *Read length*: The length of the sequencing reads in the library. This information is required only for paired-end sequencing data
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225
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226 *Additional options*: refer to lumpy-sv_ documentation and the publication (doi 10.1186/gb-2014-15-6-r84)
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227
1
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228 **lumpy-sv manual**
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229
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230 Read the lumpy-sv_ documentation for details on using lumpy.
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231
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232 .. _lumpy-sv: https://github.com/arq5x/lumpy-sv
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233
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234 **lumpy options**
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235
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236 v 0.2.13
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237 Author: Ryan Layer (rl6sf@virginia.edu)
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238
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239 Summary: Find structural variations in various signals.
a006d42dd759 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit bd0a0b0717fd7da2ff703668b21ff7db3677d61b
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240
a006d42dd759 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit bd0a0b0717fd7da2ff703668b21ff7db3677d61b
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241 Options::
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242 <![CDATA[
1
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243
a006d42dd759 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit bd0a0b0717fd7da2ff703668b21ff7db3677d61b
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244 -g Genome file (defines chromosome order)
a006d42dd759 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit bd0a0b0717fd7da2ff703668b21ff7db3677d61b
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245 -e Show evidence for each call
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246 -w File read windows size (default 1000000)
a006d42dd759 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit bd0a0b0717fd7da2ff703668b21ff7db3677d61b
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247 -mw minimum weight for a call
a006d42dd759 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit bd0a0b0717fd7da2ff703668b21ff7db3677d61b
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248 -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
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249 -tt trim threshold
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250 -x exclude file bed file
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251 -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
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252 -P output probability curve for each variant
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253 -b output BEDPE instead of VCF
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254 -sr bam_file:<file name>,
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255 id:<sample name>,
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256 back_distance:<distance>,
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257 min_mapping_threshold:<mapping quality>,
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258 weight:<sample weight>,
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259 min_clip:<minimum clip length>,
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260 read_group:<string>
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261
5
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262 -pe bam_file:<file name>,
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263 id:<sample name>,
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264 histo_file:<file name>,
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265 mean:<value>,
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266 stdev:<value>,
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267 read_length:<length>,
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268 min_non_overlap:<length>,
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269 discordant_z:<z value>,
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270 back_distance:<distance>,
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271 min_mapping_threshold:<mapping quality>,
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272 weight:<sample weight>,
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273 read_group:<string>
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274
5
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275 -bedpe bedpe_file:<bedpe file>,
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276 id:<sample name>,
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277 weight:<sample weight>
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278 ]]>
0
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279 </help>
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280
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281 <citations>
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282 <citation type="doi">10.1186/gb-2014-15-6-r84</citation>
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283 </citations>
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284 </tool>