Mercurial > repos > drosofff > lumpy
comparison lumpy.xml @ 4:2f41fac75575 draft
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 |
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| 3:0bd777f0d6d8 | 4:2f41fac75575 |
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| 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" /> |