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comparison lumpy.xml @ 4:2f41fac75575 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 66d42b0d63ff5d72c6611106ed3366a58c73a55d
author drosofff
date Wed, 07 Dec 2016 09:52:03 -0500
parents 0bd777f0d6d8
children 745cbe841e40
comparison
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3:0bd777f0d6d8 4:2f41fac75575
23 samtools view -b -F 1294 input.bam > "input.discordants.unsorted.bam" && 23 samtools view -b -F 1294 input.bam > "input.discordants.unsorted.bam" &&
24 samtools view -h input.bam | python $__tool_directory__/extractSplitReads_BwaMem.py -i stdin | samtools view -Sb - > "input.splitters.unsorted.bam" && 24 samtools view -h input.bam | python $__tool_directory__/extractSplitReads_BwaMem.py -i stdin | samtools view -Sb - > "input.splitters.unsorted.bam" &&
25 samtools sort input.discordants.unsorted.bam > input.discordants.bam && 25 samtools sort input.discordants.unsorted.bam > input.discordants.bam &&
26 samtools sort input.splitters.unsorted.bam > input.splitters.bam && 26 samtools sort input.splitters.unsorted.bam > input.splitters.bam &&
27 samtools view -r readgroup input.bam 27 samtools view -r readgroup input.bam
28 |tail -n +$seq_method.additional_params.samplingValue 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 $seq_method.additional_params.tt
33 -pe id:input.bam,bam_file:input.discordants.bam,histo_file:input.lib.histo,mean:"\$mean",stdev:"\$stdev",read_length:$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:$seq_method.additional_params.min_mapping_threshold 33 -pe id:input.bam,bam_file:input.discordants.bam,histo_file:input.lib.histo,mean:"\$mean",stdev:"\$stdev",read_length:$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:$seq_method.additional_params.min_mapping_threshold
56 samtools sort input.A.discordants.unsorted.bam > input.A.discordants.bam && 56 samtools sort input.A.discordants.unsorted.bam > input.A.discordants.bam &&
57 samtools sort input.B.discordants.unsorted.bam > input.B.discordants.bam && 57 samtools sort input.B.discordants.unsorted.bam > input.B.discordants.bam &&
58 samtools sort input.A.splitters.unsorted.bam > input.A.splitters.bam && 58 samtools sort input.A.splitters.unsorted.bam > input.A.splitters.bam &&
59 samtools sort input.B.splitters.unsorted.bam > input.B.splitters.bam && 59 samtools sort input.B.splitters.unsorted.bam > input.B.splitters.bam &&
60 samtools view -r readgroup input.A.bam 60 samtools view -r readgroup input.A.bam
61 |tail -n +$seq_method.additional_params.samplingValue 61 |tail -n +1
62 |python $__tool_directory__/pairend_distro.py -r 101 -X 4 -N $seq_method.additional_params.samplingValue -o input.A.lib.histo > meandevA.txt && 62 |python $__tool_directory__/pairend_distro.py -r 101 -X 4 -N $seq_method.additional_params.samplingValue -o input.A.lib.histo > meandevA.txt &&
63 samtools view -r readgroup input.B.bam 63 samtools view -r readgroup input.B.bam
64 |tail -n +$seq_method.additional_params.samplingValue 64 |tail -n +1
65 |python $__tool_directory__/pairend_distro.py -r 101 -X 4 -N $seq_method.additional_params.samplingValue -o input.B.lib.histo > meandevB.txt && 65 |python $__tool_directory__/pairend_distro.py -r 101 -X 4 -N $seq_method.additional_params.samplingValue -o input.B.lib.histo > meandevB.txt &&
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://) &&
144 </conditional> 144 </conditional>
145 145
146 </inputs> 146 </inputs>
147 147
148 <outputs> 148 <outputs>
149 <data format="tabular" name="histogram" type="data" label="Lumpy on ${analysis_type.input_file.element_identifier}: Fragment size distribution"> 149 <data format="tabular" name="histogram" label="Lumpy on ${analysis_type.input_file.element_identifier}: Fragment size distribution">
150 <filter>seq_method['seq_method_list'] == "paired-end"</filter> 150 <filter>seq_method['seq_method_list'] == "paired-end"</filter>
151 </data> 151 </data>
152 <data format="tabular" name="histogramB" type="data" label="Lumpy on ${analysis_type.input_fileB.element_identifier}: Fragment size distribution"> 152 <data format="tabular" name="histogramB" label="Lumpy on ${analysis_type.input_fileB.element_identifier}: Fragment size distribution">
153 <filter>seq_method['seq_method_list'] == "paired-end"</filter> 153 <filter>seq_method['seq_method_list'] == "paired-end"</filter>
154 <filter>analysis_type['analysis_type_list'] == "two_sample"</filter> 154 <filter>analysis_type['analysis_type_list'] == "two_sample"</filter>
155 </data> 155 </data>
156 <data format="bam" name="splits" type="data" label="Lumpy on ${analysis_type.input_file.element_identifier}: Split Reads (Bam format)"/> 156 <data format="bam" name="splits" label="Lumpy on ${analysis_type.input_file.element_identifier}: Split Reads (Bam format)"/>
157 <data format="bam" name="splitsB" type="data" label="Lumpy on ${analysis_type.input_fileB.element_identifier}: Split Reads (Bam format)"> 157 <data format="bam" name="splitsB" label="Lumpy on ${analysis_type.input_fileB.element_identifier}: Split Reads (Bam format)">
158 <filter>analysis_type['analysis_type_list'] == "two_sample"</filter> 158 <filter>analysis_type['analysis_type_list'] == "two_sample"</filter>
159 </data> 159 </data>
160 <data format="bam" name="discordants" type="data" label="Lumpy on ${analysis_type.input_file.element_identifier}: Discordant Pairs (Bam format)"> 160 <data format="bam" name="discordants" label="Lumpy on ${analysis_type.input_file.element_identifier}: Discordant Pairs (Bam format)">
161 <filter>seq_method['seq_method_list'] == "paired-end"</filter> 161 <filter>seq_method['seq_method_list'] == "paired-end"</filter>
162 </data> 162 </data>
163 <data format="bam" name="discordantsB" type="data" label="Lumpy on ${analysis_type.input_fileB.element_identifier}: Discordant Pairs (Bam format)"> 163 <data format="bam" name="discordantsB" label="Lumpy on ${analysis_type.input_fileB.element_identifier}: Discordant Pairs (Bam format)">
164 <filter>seq_method['seq_method_list'] == "paired-end"</filter> 164 <filter>seq_method['seq_method_list'] == "paired-end"</filter>
165 <filter>analysis_type['analysis_type_list'] == "two_sample"</filter> 165 <filter>analysis_type['analysis_type_list'] == "two_sample"</filter>
166 </data> 166 </data>
167 <data format="vcf" name="vcf_call" type="data" label="Lumpy Variant Calling (vcf format)"/> 167 <data format="vcf" name="vcf_call" label="Lumpy Variant Calling (vcf format)"/>
168 </outputs> 168 </outputs>
169 169
170 <tests> 170 <tests>
171 <test> 171 <test>
172 <param name="analysis_type" value="one_sample" /> 172 <param name="analysis_type" value="one_sample" />