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comparison 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
comparison
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6:e9db5497e675 7:e833b178b94b
27 samtools view -r readgroup input.bam 27 samtools view -r readgroup input.bam
28 |tail -n +1 28 |tail -n +1
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 #if $output_format == "BEDPE":
34 -b
35 #end if
33 -pe id:input.bam,bam_file:input.discordants.bam,histo_file:input.lib.histo,mean:"\$mean",stdev:"\$stdev",read_length:$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:$seq_method.additional_params.min_mapping_threshold 36 -pe id:input.bam,bam_file:input.discordants.bam,histo_file:input.lib.histo,mean:"\$mean",stdev:"\$stdev",read_length:$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:$seq_method.additional_params.min_mapping_threshold
34 -sr id:input.bam,bam_file:input.splitters.bam,back_distance:$seq_method.additional_params.back_distance,weight:$seq_method.additional_params.weight,min_mapping_threshold:$seq_method.additional_params.min_mapping_threshold > output.vcf && 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 &&
35 mv input.discordants.bam $discordants && 38 mv input.discordants.bam $discordants &&
36 mv input.splitters.bam $splits && 39 mv input.splitters.bam $splits &&
37 mv input.lib.histo $histogram && 40 mv input.lib.histo $histogram &&
39 rm input.discordants.unsorted.bam input.splitters.unsorted.bam meandev.txt 42 rm input.discordants.unsorted.bam input.splitters.unsorted.bam meandev.txt
40 #end if 43 #end if
41 #if $seq_method.seq_method_list == "single-read": 44 #if $seq_method.seq_method_list == "single-read":
42 samtools view -h input.bam | python $__tool_directory__/extractSplitReads_BwaMem.py -i stdin | samtools view -Sb - > "input.splitters.unsorted.bam" && 45 samtools view -h input.bam | python $__tool_directory__/extractSplitReads_BwaMem.py -i stdin | samtools view -Sb - > "input.splitters.unsorted.bam" &&
43 lumpy -mw $seq_method.additional_params.mw -tt $seq_method.additional_params.tt 46 lumpy -mw $seq_method.additional_params.mw -tt $seq_method.additional_params.tt
47 #if $output_format == "BEDPE":
48 -b
49 #end if
44 -sr id:input.bam,bam_file:input.splitters.unsorted.bam,back_distance:$seq_method.additional_params.back_distance,weight:$seq_method.additional_params.weight,min_mapping_threshold:$seq_method.additional_params.min_mapping_threshold > output.vcf && 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 &&
45 mv input.splitters.unsorted.bam $splits && 51 mv input.splitters.unsorted.bam $splits &&
46 mv output.vcf $vcf_call 52 mv output.vcf $vcf_call
47 #end if 53 #end if
48 54
66 meanA=\$(cat meandevA.txt | sed s/mean:// | sed -r s/stdev:.+//) && 72 meanA=\$(cat meandevA.txt | sed s/mean:// | sed -r s/stdev:.+//) &&
67 meanB=\$(cat meandevB.txt | sed s/mean:// | sed -r s/stdev:.+//) && 73 meanB=\$(cat meandevB.txt | sed s/mean:// | sed -r s/stdev:.+//) &&
68 stdevA=\$(cat meandevA.txt | sed -r s/mean:.+stdev://) && 74 stdevA=\$(cat meandevA.txt | sed -r s/mean:.+stdev://) &&
69 stdevB=\$(cat meandevB.txt | sed -r s/mean:.+stdev://) && 75 stdevB=\$(cat meandevB.txt | sed -r s/mean:.+stdev://) &&
70 lumpy -mw $seq_method.additional_params.mw -tt $seq_method.additional_params.tt 76 lumpy -mw $seq_method.additional_params.mw -tt $seq_method.additional_params.tt
77 #if $output_format == "BEDPE":
78 -b
79 #end if
71 -pe id:inputA.bam,bam_file:input.A.discordants.bam,histo_file:input.A.lib.histo,mean:"\$meanA",stdev:"\$stdevA",read_length:$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:$seq_method.additional_params.min_mapping_threshold 80 -pe id:inputA.bam,bam_file:input.A.discordants.bam,histo_file:input.A.lib.histo,mean:"\$meanA",stdev:"\$stdevA",read_length:$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:$seq_method.additional_params.min_mapping_threshold
72 -pe id:inputB.bam,bam_file:input.B.discordants.bam,histo_file:input.B.lib.histo,mean:"\$meanB",stdev:"\$stdevA",read_length:$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:$seq_method.additional_params.min_mapping_threshold 81 -pe id:inputB.bam,bam_file:input.B.discordants.bam,histo_file:input.B.lib.histo,mean:"\$meanB",stdev:"\$stdevA",read_length:$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:$seq_method.additional_params.min_mapping_threshold
73 -sr id:inputA.bam,bam_file:input.A.splitters.bam,back_distance:$seq_method.additional_params.back_distance,weight:$seq_method.additional_params.weight,min_mapping_threshold:$seq_method.additional_params.min_mapping_threshold 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:$seq_method.additional_params.min_mapping_threshold
74 -sr id:inputB.bam,bam_file:input.B.splitters.bam,back_distance:$seq_method.additional_params.back_distance,weight:$seq_method.additional_params.weight,min_mapping_threshold:$seq_method.additional_params.min_mapping_threshold > output.vcf && 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 &&
75 mv input.A.discordants.bam $discordants && 84 mv input.A.discordants.bam $discordants &&
83 #end if 92 #end if
84 #if $seq_method.seq_method_list == "single-read": 93 #if $seq_method.seq_method_list == "single-read":
85 samtools view -h input.A.bam | python $__tool_directory__/extractSplitReads_BwaMem.py -i stdin | samtools view -Sb - > "input.A.splitters.unsorted.bam" && 94 samtools view -h input.A.bam | python $__tool_directory__/extractSplitReads_BwaMem.py -i stdin | samtools view -Sb - > "input.A.splitters.unsorted.bam" &&
86 samtools view -h input.B.bam | python $__tool_directory__/extractSplitReads_BwaMem.py -i stdin | samtools view -Sb - > "input.B.splitters.unsorted.bam" && 95 samtools view -h input.B.bam | python $__tool_directory__/extractSplitReads_BwaMem.py -i stdin | samtools view -Sb - > "input.B.splitters.unsorted.bam" &&
87 lumpy -mw $seq_method.additional_params.mw -tt $seq_method.additional_params.tt 96 lumpy -mw $seq_method.additional_params.mw -tt $seq_method.additional_params.tt
97 #if $output_format == "BEDPE":
98 -b
99 #end if
88 -sr id:input.A.bam,bam_file:input.A.splitters.unsorted.bam,back_distance:$seq_method.additional_params.back_distance,weight:$seq_method.additional_params.weight,min_mapping_threshold:$seq_method.additional_params.min_mapping_threshold 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:$seq_method.additional_params.min_mapping_threshold
89 -sr id:input.B.bam,bam_file:input.B.splitters.unsorted.bam,back_distance:$seq_method.additional_params.back_distance,weight:$seq_method.additional_params.weight,min_mapping_threshold:$seq_method.additional_params.min_mapping_threshold > output.vcf && 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 &&
90 mv input.A.splitters.unsorted.bam $splits && 102 mv input.A.splitters.unsorted.bam $splits &&
91 mv input.B.splitters.unsorted.bam $splitsB && 103 mv input.B.splitters.unsorted.bam $splitsB &&
92 mv output.vcf $vcf_call 104 mv output.vcf $vcf_call
140 <param name="min_mapping_threshold" value="20" type="integer" label="min_mapping_threshold" help="e.g. 20" /> 152 <param name="min_mapping_threshold" value="20" type="integer" label="min_mapping_threshold" help="e.g. 20" />
141 </section> 153 </section>
142 </when> 154 </when>
143 155
144 </conditional> 156 </conditional>
145 157 <param help="get variant calling in vcf or BEDPE format" label="variant calling format" name="output_format" type="select">
158 <option selected="True" value="vcf">vcf</option>
159 <option value="BEDPE">BEDPE</option>
160 </param>
146 </inputs> 161 </inputs>
147 162
148 <outputs> 163 <outputs>
149 <data format="tabular" name="histogram" label="Lumpy on ${on_string}: Fragment size distribution"> 164 <data format="tabular" name="histogram" label="Lumpy on ${on_string}: Fragment size distribution">
150 <filter>seq_method['seq_method_list'] == "paired-end"</filter> 165 <filter>seq_method['seq_method_list'] == "paired-end"</filter>
162 </data> 177 </data>
163 <data format="bam" name="discordantsB" label="Lumpy on ${on_string}: Discordant Pairs (Bam format)"> 178 <data format="bam" name="discordantsB" label="Lumpy on ${on_string}: Discordant Pairs (Bam format)">
164 <filter>seq_method['seq_method_list'] == "paired-end"</filter> 179 <filter>seq_method['seq_method_list'] == "paired-end"</filter>
165 <filter>analysis_type['analysis_type_list'] == "two_sample"</filter> 180 <filter>analysis_type['analysis_type_list'] == "two_sample"</filter>
166 </data> 181 </data>
167 <data format="vcf" name="vcf_call" label="Lumpy Variant Calling (vcf format)"/> 182 <data format="vcf" name="vcf_call" label="Lumpy Variant Calling">
183 <change_format>
184 <when format="tabular" input="output_format" value="BEDPE" />
185 </change_format>
186 </data>
168 </outputs> 187 </outputs>
169 188
170 <tests> 189 <tests>
171 <test> 190 <test>
172 <param name="analysis_type" value="one_sample" /> 191 <param name="analysis_type" value="one_sample" />