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annotate lumpy.xml @ 7:e833b178b94b draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 834a0ca8b5cc29307a03c1b22a372152ed064abd
author drosofff
date Fri, 09 Dec 2016 06:13:27 -0500
parents e9db5497e675
children 382ffb8e0caa
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b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
drosofff
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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
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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>
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
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11 <version_command>lumpy --version</version_command>
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745cbe841e40 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit ccfbe9e77653393089624d308873496d1d7e32a7
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12 <command detect_errors="exit_code"><![CDATA[
2
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
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13 #if $analysis_type.analysis_type_list == "one_sample":
5
745cbe841e40 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit ccfbe9e77653393089624d308873496d1d7e32a7
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14 ln -f -s '$analysis_type.input_file' input.bam &&
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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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15 #else:
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745cbe841e40 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit ccfbe9e77653393089624d308873496d1d7e32a7
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16 ln -f -s '$analysis_type.input_file' input.A.bam &&
745cbe841e40 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit ccfbe9e77653393089624d308873496d1d7e32a7
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17 ln -f -s '$analysis_type.input_fileB' input.B.bam &&
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8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
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18 #end if
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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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19
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
drosofff
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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
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21
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
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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
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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
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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
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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
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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
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27 samtools view -r readgroup input.bam
4
2f41fac75575 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 66d42b0d63ff5d72c6611106ed3366a58c73a55d
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28 |tail -n +1
2
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
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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
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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
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31 stdev=\$(cat meandev.txt | sed -r s/mean:.+stdev://) &&
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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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32 lumpy -mw $seq_method.additional_params.mw -tt $seq_method.additional_params.tt
e833b178b94b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 834a0ca8b5cc29307a03c1b22a372152ed064abd
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33 #if $output_format == "BEDPE":
e833b178b94b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 834a0ca8b5cc29307a03c1b22a372152ed064abd
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34 -b
e833b178b94b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 834a0ca8b5cc29307a03c1b22a372152ed064abd
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35 #end if
3
0bd777f0d6d8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 336e603ddd23f30f60f1cc40a4e8e1629d467055
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36 -pe id:input.bam,bam_file:input.discordants.bam,histo_file:input.lib.histo,mean:"\$mean",stdev:"\$stdev",read_length:$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:$seq_method.additional_params.min_mapping_threshold
2
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
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37 -sr id:input.bam,bam_file:input.splitters.bam,back_distance:$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
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38 mv input.discordants.bam $discordants &&
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
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39 mv input.splitters.bam $splits &&
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
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40 mv input.lib.histo $histogram &&
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
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41 mv output.vcf $vcf_call &&
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
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42 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
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43 #end if
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
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44 #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
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45 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
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46 lumpy -mw $seq_method.additional_params.mw -tt $seq_method.additional_params.tt
7
e833b178b94b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 834a0ca8b5cc29307a03c1b22a372152ed064abd
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47 #if $output_format == "BEDPE":
e833b178b94b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 834a0ca8b5cc29307a03c1b22a372152ed064abd
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48 -b
e833b178b94b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 834a0ca8b5cc29307a03c1b22a372152ed064abd
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49 #end if
2
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
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50 -sr id:input.bam,bam_file:input.splitters.unsorted.bam,back_distance:$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
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51 mv input.splitters.unsorted.bam $splits &&
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
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52 mv output.vcf $vcf_call
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
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53 #end if
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
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54
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
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55 #else:
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
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56
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
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57 #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
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58 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
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59 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
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60 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
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61 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
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62 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
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63 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
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64 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
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65 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
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66 samtools view -r readgroup input.A.bam
4
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67 |tail -n +1
2
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
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68 |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
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69 samtools view -r readgroup input.B.bam
4
2f41fac75575 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 66d42b0d63ff5d72c6611106ed3366a58c73a55d
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70 |tail -n +1
2
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
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71 |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
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72 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
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73 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
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74 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
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75 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
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76 lumpy -mw $seq_method.additional_params.mw -tt $seq_method.additional_params.tt
7
e833b178b94b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 834a0ca8b5cc29307a03c1b22a372152ed064abd
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77 #if $output_format == "BEDPE":
e833b178b94b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 834a0ca8b5cc29307a03c1b22a372152ed064abd
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78 -b
e833b178b94b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 834a0ca8b5cc29307a03c1b22a372152ed064abd
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79 #end if
3
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80 -pe id:inputA.bam,bam_file:input.A.discordants.bam,histo_file:input.A.lib.histo,mean:"\$meanA",stdev:"\$stdevA",read_length:$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:$seq_method.additional_params.min_mapping_threshold
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81 -pe id:inputB.bam,bam_file:input.B.discordants.bam,histo_file:input.B.lib.histo,mean:"\$meanB",stdev:"\$stdevA",read_length:$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:$seq_method.additional_params.min_mapping_threshold
2
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82 -sr id:inputA.bam,bam_file:input.A.splitters.bam,back_distance:$seq_method.additional_params.back_distance,weight:$seq_method.additional_params.weight,min_mapping_threshold:$seq_method.additional_params.min_mapping_threshold
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83 -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 &&
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84 mv input.A.discordants.bam $discordants &&
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85 mv input.B.discordants.bam $discordantsB &&
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86 mv input.A.splitters.bam $splits &&
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87 mv input.B.splitters.bam $splitsB &&
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88 mv input.A.lib.histo $histogram &&
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89 mv input.B.lib.histo $histogramB &&
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90 mv output.vcf $vcf_call &&
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91 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
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92 #end if
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93 #if $seq_method.seq_method_list == "single-read":
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94 samtools view -h input.A.bam | python $__tool_directory__/extractSplitReads_BwaMem.py -i stdin | samtools view -Sb - > "input.A.splitters.unsorted.bam" &&
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95 samtools view -h input.B.bam | python $__tool_directory__/extractSplitReads_BwaMem.py -i stdin | samtools view -Sb - > "input.B.splitters.unsorted.bam" &&
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96 lumpy -mw $seq_method.additional_params.mw -tt $seq_method.additional_params.tt
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97 #if $output_format == "BEDPE":
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98 -b
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99 #end if
2
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100 -sr id:input.A.bam,bam_file:input.A.splitters.unsorted.bam,back_distance:$seq_method.additional_params.back_distance,weight:$seq_method.additional_params.weight,min_mapping_threshold:$seq_method.additional_params.min_mapping_threshold
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101 -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 &&
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102 mv input.A.splitters.unsorted.bam $splits &&
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103 mv input.B.splitters.unsorted.bam $splitsB &&
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104 mv output.vcf $vcf_call
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105 #end if
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106
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107
0
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108 #end if
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109
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110 ]]></command>
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111 <!-- basic error handling -->
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112 <inputs>
2
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113 <conditional name="analysis_type">
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114 <param help="Single or paired conditions (eg tumor vs normal)" label="Input(s)" name="analysis_type_list" type="select">
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115 <option selected="True" value="one_sample">One Sample</option>
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116 <option value="two_sample">Two samples</option>
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117 </param>
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118 <when value="one_sample">
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119 <param format="bam" name="input_file" type="data" label="One BAM alignment file produced by BWA-mem"/>
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120 <param name="readLength" value="151" type="integer" label="read length" help="e.g. 151 nt" />
2
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121 </when>
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122 <when value="two_sample">
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123 <param format="bam" name="input_file" type="data" label="One BAM alignment file produced by BWA-mem"/>
3
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124 <param name="readLength" value="151" type="integer" label="read length" help="e.g. 151 nt" />
2
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125 <param format="bam" name="input_fileB" type="data" label="One BAM alignment file produced by BWA-mem"/>
3
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126 <param name="readLengthB" value="151" type="integer" label="read length" help="e.g. 151 nt" />
2
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127 </when>
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128 </conditional>
0
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129 <conditional name="seq_method">
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130 <param help="Paired-end or single-read sequencing" label="Sequencing method" name="seq_method_list" type="select">
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131 <option selected="True" value="paired-end">Paired-end sequencing</option>
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132 <option value="single-read">Single-read sequencing</option>
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133 </param>
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134 <when value="paired-end">
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135 <section name="additional_params" title="Additional Options" expanded="False">
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136 <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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137 <param name="mw" value="4" type="integer" label="-mw" help="minimum weight across all samples for a call (default: 4)" />
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138 <param name="tt" value="0" type="integer" label="-tt" help="trim threshold (default: 0)" />
0
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139 <param name="min_non_overlap" value="101" type="integer" label="min_non_overlap" help="e.g. 101" />
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140 <param name="discordant_z" value="5" type="integer" label="discordant_z" help="e.g. 5" />
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141 <param name="back_distance" value="10" type="integer" label="back_distance" help="e.g. 10" />
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142 <param name="weight" value="1" type="integer" label="weight" help="e.g. 1" />
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143 <param name="min_mapping_threshold" value="20" type="integer" label="min_mapping_threshold" help="e.g. 20" />
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144 </section>
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145 </when>
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146 <when value="single-read">
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147 <section name="additional_params" title="Additional Options" expanded="False">
2
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148 <param name="mw" value="4" type="integer" label="-mw" help="minimum weight across all samples for a call (default: 4)" />
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149 <param name="tt" value="0" type="integer" label="-tt" help="trim threshold (default: 0)" />
0
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150 <param name="back_distance" value="10" type="integer" label="back_distance" help="e.g. 10" />
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151 <param name="weight" value="1" type="integer" label="weight" help="e.g. 1" />
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152 <param name="min_mapping_threshold" value="20" type="integer" label="min_mapping_threshold" help="e.g. 20" />
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153 </section>
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154 </when>
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155
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156 </conditional>
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157 <param help="get variant calling in vcf or BEDPE format" label="variant calling format" name="output_format" type="select">
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158 <option selected="True" value="vcf">vcf</option>
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159 <option value="BEDPE">BEDPE</option>
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160 </param>
0
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161 </inputs>
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162
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163 <outputs>
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164 <data format="tabular" name="histogram" label="Lumpy on ${on_string}: Fragment size distribution">
0
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165 <filter>seq_method['seq_method_list'] == "paired-end"</filter>
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166 </data>
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167 <data format="tabular" name="histogramB" label="Lumpy on ${on_string}: Fragment size distribution">
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168 <filter>seq_method['seq_method_list'] == "paired-end"</filter>
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169 <filter>analysis_type['analysis_type_list'] == "two_sample"</filter>
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170 </data>
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171 <data format="bam" name="splits" label="Lumpy on ${on_string}: Split Reads (Bam format)"/>
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172 <data format="bam" name="splitsB" label="Lumpy on ${on_string}: Split Reads (Bam format)">
2
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173 <filter>analysis_type['analysis_type_list'] == "two_sample"</filter>
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174 </data>
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175 <data format="bam" name="discordants" label="Lumpy on ${on_string}: Discordant Pairs (Bam format)">
0
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176 <filter>seq_method['seq_method_list'] == "paired-end"</filter>
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177 </data>
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178 <data format="bam" name="discordantsB" label="Lumpy on ${on_string}: Discordant Pairs (Bam format)">
2
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179 <filter>seq_method['seq_method_list'] == "paired-end"</filter>
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180 <filter>analysis_type['analysis_type_list'] == "two_sample"</filter>
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181 </data>
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182 <data format="vcf" name="vcf_call" label="Lumpy Variant Calling">
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183 <change_format>
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184 <when format="tabular" input="output_format" value="BEDPE" />
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185 </change_format>
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186 </data>
0
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187 </outputs>
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188
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189 <tests>
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190 <test>
2
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191 <param name="analysis_type" value="one_sample" />
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192 <param name="input_file" value="sr.input.bam" ftype="bam"/>
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193 <param name="seq_method_list" value="single-read" />
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194 <param name="mw" value="4"/>
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195 <param name="tt" value="0"/>
0
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196 <param name="back_distance" value="10"/>
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197 <param name="weight" value="1" />
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198 <param name="min_mapping_threshold" value="20" />
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199 <output name="vcf_call" file="output.vcf" ftype="vcf"/>
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200 </test>
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201 </tests>
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202
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203 <help>
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204
3
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205 **Input(s)**
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206
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207 *One sample* : lumpy search structural variations inside a single sequencing dataset
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208
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209 *Two samples*: lumpy search structural variations inside and across two sequencing datasets from two samples
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210
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211 Analysis of sample replicates is not implemented yet in this wrapper
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212
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213 *BAM files*: Only BAM alignments produced by BWA-mem have been tested with this tool
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214
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215 **Sequencing method**
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216
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217 *Paired-end sequencing*: Both ends of library fragments have been sequenced, resulting in two paired sequencing datasets
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218
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219 *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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220
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221 *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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222
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223 *Additional options*: refer to lumpy-sv_ documentation and the publication (doi 10.1186/gb-2014-15-6-r84)
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224
1
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225 **lumpy-sv manual**
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226
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227 Read the lumpy-sv_ documentation for details on using lumpy.
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228
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229 .. _lumpy-sv: https://github.com/arq5x/lumpy-sv
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230
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231 **lumpy options**
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232
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233 v 0.2.13
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234 Author: Ryan Layer (rl6sf@virginia.edu)
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235
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236 Summary: Find structural variations in various signals.
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237
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238 Options::
5
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239 <![CDATA[
1
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240
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241 -g Genome file (defines chromosome order)
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242 -e Show evidence for each call
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243 -w File read windows size (default 1000000)
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244 -mw minimum weight for a call
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245 -msw minimum per-sample weight for a call
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246 -tt trim threshold
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247 -x exclude file bed file
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248 -t temp file prefix, must be to a writeable directory
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249 -P output probability curve for each variant
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250 -b output BEDPE instead of VCF
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251 -sr bam_file:<file name>,
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252 id:<sample name>,
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253 back_distance:<distance>,
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254 min_mapping_threshold:<mapping quality>,
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255 weight:<sample weight>,
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256 min_clip:<minimum clip length>,
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257 read_group:<string>
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258
5
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259 -pe bam_file:<file name>,
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260 id:<sample name>,
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261 histo_file:<file name>,
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262 mean:<value>,
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263 stdev:<value>,
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264 read_length:<length>,
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265 min_non_overlap:<length>,
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266 discordant_z:<z value>,
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267 back_distance:<distance>,
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268 min_mapping_threshold:<mapping quality>,
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269 weight:<sample weight>,
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270 read_group:<string>
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271
5
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272 -bedpe bedpe_file:<bedpe file>,
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273 id:<sample name>,
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274 weight:<sample weight>
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275 ]]>
0
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276 </help>
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277
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278 <citations>
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279 <citation type="doi">10.1186/gb-2014-15-6-r84</citation>
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280 </citations>
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281 </tool>