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comparison lumpy.xml @ 3:0bd777f0d6d8 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 336e603ddd23f30f60f1cc40a4e8e1629d467055
author drosofff
date Wed, 07 Dec 2016 05:26:21 -0500
parents b1e152172de9
children 2f41fac75575
comparison
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2:b1e152172de9 3:0bd777f0d6d8
28 |tail -n +$seq_method.additional_params.samplingValue 28 |tail -n +$seq_method.additional_params.samplingValue
29 |python $__tool_directory__/pairend_distro.py -r 101 -X 4 -N $seq_method.additional_params.samplingValue -o input.lib.histo > meandev.txt && 29 |python $__tool_directory__/pairend_distro.py -r 101 -X 4 -N $seq_method.additional_params.samplingValue -o input.lib.histo > meandev.txt &&
30 mean=\$(cat meandev.txt | sed s/mean:// | sed -r s/stdev:.+//) && 30 mean=\$(cat meandev.txt | sed s/mean:// | sed -r s/stdev:.+//) &&
31 stdev=\$(cat meandev.txt | sed -r s/mean:.+stdev://) && 31 stdev=\$(cat meandev.txt | sed -r s/mean:.+stdev://) &&
32 lumpy -mw $seq_method.additional_params.mw -tt $seq_method.additional_params.tt 32 lumpy -mw $seq_method.additional_params.mw -tt $seq_method.additional_params.tt
33 -pe id:input.bam,bam_file:input.discordants.bam,histo_file:input.lib.histo,mean:"\$mean",stdev:"\$stdev",read_length:$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:$seq_method.additional_params.min_mapping_threshold 33 -pe id:input.bam,bam_file:input.discordants.bam,histo_file:input.lib.histo,mean:"\$mean",stdev:"\$stdev",read_length:$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:$seq_method.additional_params.min_mapping_threshold
34 -sr id:input.bam,bam_file:input.splitters.bam,back_distance:$seq_method.additional_params.back_distance,weight:$seq_method.additional_params.weight,min_mapping_threshold:$seq_method.additional_params.min_mapping_threshold > output.vcf && 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 &&
35 mv input.discordants.bam $discordants && 35 mv input.discordants.bam $discordants &&
36 mv input.splitters.bam $splits && 36 mv input.splitters.bam $splits &&
37 mv input.lib.histo $histogram && 37 mv input.lib.histo $histogram &&
38 mv output.vcf $vcf_call && 38 mv output.vcf $vcf_call &&
66 meanA=\$(cat meandevA.txt | sed s/mean:// | sed -r s/stdev:.+//) && 66 meanA=\$(cat meandevA.txt | sed s/mean:// | sed -r s/stdev:.+//) &&
67 meanB=\$(cat meandevB.txt | sed s/mean:// | sed -r s/stdev:.+//) && 67 meanB=\$(cat meandevB.txt | sed s/mean:// | sed -r s/stdev:.+//) &&
68 stdevA=\$(cat meandevA.txt | sed -r s/mean:.+stdev://) && 68 stdevA=\$(cat meandevA.txt | sed -r s/mean:.+stdev://) &&
69 stdevB=\$(cat meandevB.txt | sed -r s/mean:.+stdev://) && 69 stdevB=\$(cat meandevB.txt | sed -r s/mean:.+stdev://) &&
70 lumpy -mw $seq_method.additional_params.mw -tt $seq_method.additional_params.tt 70 lumpy -mw $seq_method.additional_params.mw -tt $seq_method.additional_params.tt
71 -pe id:inputA.bam,bam_file:input.A.discordants.bam,histo_file:input.A.lib.histo,mean:"\$meanA",stdev:"\$stdevA",read_length:$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:$seq_method.additional_params.min_mapping_threshold 71 -pe id:inputA.bam,bam_file:input.A.discordants.bam,histo_file:input.A.lib.histo,mean:"\$meanA",stdev:"\$stdevA",read_length:$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:$seq_method.additional_params.min_mapping_threshold
72 -pe id:inputB.bam,bam_file:input.B.discordants.bam,histo_file:input.B.lib.histo,mean:"\$meanB",stdev:"\$stdevA",read_length:$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:$seq_method.additional_params.min_mapping_threshold 72 -pe id:inputB.bam,bam_file:input.B.discordants.bam,histo_file:input.B.lib.histo,mean:"\$meanB",stdev:"\$stdevA",read_length:$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:$seq_method.additional_params.min_mapping_threshold
73 -sr id:inputA.bam,bam_file:input.A.splitters.bam,back_distance:$seq_method.additional_params.back_distance,weight:$seq_method.additional_params.weight,min_mapping_threshold:$seq_method.additional_params.min_mapping_threshold 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:$seq_method.additional_params.min_mapping_threshold
74 -sr id:inputB.bam,bam_file:input.B.splitters.bam,back_distance:$seq_method.additional_params.back_distance,weight:$seq_method.additional_params.weight,min_mapping_threshold:$seq_method.additional_params.min_mapping_threshold > output.vcf && 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 &&
75 mv input.A.discordants.bam $discordants && 75 mv input.A.discordants.bam $discordants &&
76 mv input.B.discordants.bam $discordantsB && 76 mv input.B.discordants.bam $discordantsB &&
77 mv input.A.splitters.bam $splits && 77 mv input.A.splitters.bam $splits &&
97 97
98 ]]></command> 98 ]]></command>
99 <!-- basic error handling --> 99 <!-- basic error handling -->
100 <inputs> 100 <inputs>
101 <conditional name="analysis_type"> 101 <conditional name="analysis_type">
102 <param help="Single or paired conditions (eg tumor vs normal)" label="Analysis type" name="analysis_type_list" type="select"> 102 <param help="Single or paired conditions (eg tumor vs normal)" label="Input(s)" name="analysis_type_list" type="select">
103 <option selected="True" value="one_sample">One Sample</option> 103 <option selected="True" value="one_sample">One Sample</option>
104 <option value="two_sample">Two samples</option> 104 <option value="two_sample">Two samples</option>
105 </param> 105 </param>
106 <when value="one_sample"> 106 <when value="one_sample">
107 <param format="bam" name="input_file" type="data" label="One BAM alignment file produced by BWA-mem"/> 107 <param format="bam" name="input_file" type="data" label="One BAM alignment file produced by BWA-mem"/>
108 <param name="readLength" value="151" type="integer" label="read length" help="e.g. 151 nt" />
108 </when> 109 </when>
109 <when value="two_sample"> 110 <when value="two_sample">
110 <param format="bam" name="input_file" type="data" label="One BAM alignment file produced by BWA-mem"/> 111 <param format="bam" name="input_file" type="data" label="One BAM alignment file produced by BWA-mem"/>
112 <param name="readLength" value="151" type="integer" label="read length" help="e.g. 151 nt" />
111 <param format="bam" name="input_fileB" type="data" label="One BAM alignment file produced by BWA-mem"/> 113 <param format="bam" name="input_fileB" type="data" label="One BAM alignment file produced by BWA-mem"/>
114 <param name="readLengthB" value="151" type="integer" label="read length" help="e.g. 151 nt" />
112 </when> 115 </when>
113 </conditional> 116 </conditional>
114 <conditional name="seq_method"> 117 <conditional name="seq_method">
115 <param help="Paired-end or single-read sequencing" label="Sequencing method" name="seq_method_list" type="select"> 118 <param help="Paired-end or single-read sequencing" label="Sequencing method" name="seq_method_list" type="select">
116 <option selected="True" value="paired-end">Paired-end sequencing</option> 119 <option selected="True" value="paired-end">Paired-end sequencing</option>
117 <option value="single-read">Single-read sequencing</option> 120 <option value="single-read">Single-read sequencing</option>
118 </param> 121 </param>
119 <when value="paired-end"> 122 <when value="paired-end">
120 <param name="readLength" value="151" type="integer" label="read length" help="e.g. 151 nt" />
121 <section name="additional_params" title="Additional Options" expanded="False"> 123 <section name="additional_params" title="Additional Options" expanded="False">
122 <param name="samplingValue" value="100000" type="integer" label="number of reads to compute mean and stdev of read length" help="e.g. 10000" /> 124 <param name="samplingValue" value="100000" type="integer" label="number of reads to compute mean and stdev of read length" help="e.g. 10000" />
123 <param name="mw" value="4" type="integer" label="-mw" help="minimum weight across all samples for a call (default: 4)" /> 125 <param name="mw" value="4" type="integer" label="-mw" help="minimum weight across all samples for a call (default: 4)" />
124 <param name="tt" value="0" type="integer" label="-tt" help="trim threshold (default: 0)" /> 126 <param name="tt" value="0" type="integer" label="-tt" help="trim threshold (default: 0)" />
125 <param name="min_non_overlap" value="101" type="integer" label="min_non_overlap" help="e.g. 101" /> 127 <param name="min_non_overlap" value="101" type="integer" label="min_non_overlap" help="e.g. 101" />
178 <output name="vcf_call" file="output.vcf" ftype="vcf"/> 180 <output name="vcf_call" file="output.vcf" ftype="vcf"/>
179 </test> 181 </test>
180 </tests> 182 </tests>
181 183
182 <help> 184 <help>
185
186 **Input(s)**
187
188 *One sample* : lumpy search structural variations inside a single sequencing dataset
189
190 *Two samples*: lumpy search structural variations inside and across two sequencing datasets from two samples
191
192 Analysis of sample replicates is not implemented yet in this wrapper
193
194 *BAM files*: Only BAM alignments produced by BWA-mem have been tested with this tool
195
196 **Sequencing method**
197
198 *Paired-end sequencing*: Both ends of library fragments have been sequenced, resulting in two paired sequencing datasets
199
200 *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
201
202 *Read length*: The length of the sequencing reads in the library. This information is required only for paired-end sequencing data
203
204 *Additional options*: refer to lumpy-sv_ documentation and the publication (doi 10.1186/gb-2014-15-6-r84)
183 205
184 **lumpy-sv manual** 206 **lumpy-sv manual**
185 207
186 Read the lumpy-sv_ documentation for details on using lumpy. 208 Read the lumpy-sv_ documentation for details on using lumpy.
187 209