Mercurial > repos > drosofff > lumpy
comparison lumpy.xml @ 8:382ffb8e0caa draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 8375ddf784506b68d28bc9e6224648fafa796d9f
author | drosofff |
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date | Sat, 10 Dec 2016 20:26:56 -0500 |
parents | e833b178b94b |
children | 43462e6e9140 |
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7:e833b178b94b | 8:382ffb8e0caa |
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6 <requirement type="package" version="1.11.2">numpy</requirement> | 6 <requirement type="package" version="1.11.2">numpy</requirement> |
7 </requirements> | 7 </requirements> |
8 <stdio> | 8 <stdio> |
9 <exit_code range="1:" level="fatal" description="Tool exception" /> | 9 <exit_code range="1:" level="fatal" description="Tool exception" /> |
10 </stdio> | 10 </stdio> |
11 <version_command>lumpy --version</version_command> | |
12 <command detect_errors="exit_code"><![CDATA[ | 11 <command detect_errors="exit_code"><![CDATA[ |
13 #if $analysis_type.analysis_type_list == "one_sample": | 12 #if $analysis_type.analysis_type_list == "one_sample": |
14 ln -f -s '$analysis_type.input_file' input.bam && | 13 ln -f -s '$analysis_type.input_file' input.bam && |
15 #else: | 14 #else: |
16 ln -f -s '$analysis_type.input_file' input.A.bam && | 15 ln -f -s '$analysis_type.input_file' input.A.bam && |
22 #if $seq_method.seq_method_list == "paired-end": | 21 #if $seq_method.seq_method_list == "paired-end": |
23 samtools view -b -F 1294 input.bam > "input.discordants.unsorted.bam" && | 22 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" && | 23 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 && | 24 samtools sort input.discordants.unsorted.bam > input.discordants.bam && |
26 samtools sort input.splitters.unsorted.bam > input.splitters.bam && | 25 samtools sort input.splitters.unsorted.bam > input.splitters.bam && |
27 samtools view -r readgroup input.bam | 26 samtools view input.bam |
28 |tail -n +1 | 27 |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 && | 28 |python $__tool_directory__/pairend_distro.py -r $readLength -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:.+//) && | 29 mean=\$(cat meandev.txt | sed s/mean:// | sed -r s/stdev:.+//) && |
31 stdev=\$(cat meandev.txt | sed -r s/mean:.+stdev://) && | 30 stdev=\$(cat meandev.txt | sed -r s/mean:.+stdev://) && |
32 lumpy -mw $seq_method.additional_params.mw -tt $seq_method.additional_params.tt | 31 lumpy -mw $seq_method.additional_params.mw -tt $seq_method.additional_params.tt |
33 #if $output_format == "BEDPE": | 32 #if $output_format == "BEDPE": |
34 -b | 33 -b |
35 #end if | 34 #end if |
36 -pe id:input.bam,bam_file:input.discordants.bam,histo_file:input.lib.histo,mean:"\$mean",stdev:"\$stdev",read_length:$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:$seq_method.additional_params.min_mapping_threshold | 35 -pe id:input.bam,bam_file:input.discordants.bam,histo_file:input.lib.histo,mean:"\$mean",stdev:"\$stdev",read_length:$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:$seq_method.additional_params.min_mapping_threshold |
37 -sr id:input.bam,bam_file:input.splitters.bam,back_distance:$seq_method.additional_params.back_distance,weight:$seq_method.additional_params.weight,min_mapping_threshold:$seq_method.additional_params.min_mapping_threshold > output.vcf && | 36 -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 && |
38 mv input.discordants.bam $discordants && | 37 mv input.discordants.bam $discordants && |
39 mv input.splitters.bam $splits && | 38 mv input.splitters.bam $splits && |
40 mv input.lib.histo $histogram && | 39 mv input.lib.histo $histogram && |
41 mv output.vcf $vcf_call && | 40 mv output.vcf $vcf_call && |
49 #end if | 48 #end if |
50 -sr id:input.bam,bam_file:input.splitters.unsorted.bam,back_distance:$seq_method.additional_params.back_distance,weight:$seq_method.additional_params.weight,min_mapping_threshold:$seq_method.additional_params.min_mapping_threshold > output.vcf && | 49 -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 && |
51 mv input.splitters.unsorted.bam $splits && | 50 mv input.splitters.unsorted.bam $splits && |
52 mv output.vcf $vcf_call | 51 mv output.vcf $vcf_call |
53 #end if | 52 #end if |
54 | 53 |
55 #else: | 54 #else: |
56 | 55 |
57 #if $seq_method.seq_method_list == "paired-end": | 56 #if $seq_method.seq_method_list == "paired-end": |
58 samtools view -b -F 1294 input.A.bam > "input.A.discordants.unsorted.bam" && | 57 samtools view -b -F 1294 input.A.bam > "input.A.discordants.unsorted.bam" && |
59 samtools view -b -F 1294 input.B.bam > "input.B.discordants.unsorted.bam" && | 58 samtools view -b -F 1294 input.B.bam > "input.B.discordants.unsorted.bam" && |
61 samtools view -h input.B.bam | python $__tool_directory__/extractSplitReads_BwaMem.py -i stdin | samtools view -Sb - > "input.B.splitters.unsorted.bam" && | 60 samtools view -h input.B.bam | python $__tool_directory__/extractSplitReads_BwaMem.py -i stdin | samtools view -Sb - > "input.B.splitters.unsorted.bam" && |
62 samtools sort input.A.discordants.unsorted.bam > input.A.discordants.bam && | 61 samtools sort input.A.discordants.unsorted.bam > input.A.discordants.bam && |
63 samtools sort input.B.discordants.unsorted.bam > input.B.discordants.bam && | 62 samtools sort input.B.discordants.unsorted.bam > input.B.discordants.bam && |
64 samtools sort input.A.splitters.unsorted.bam > input.A.splitters.bam && | 63 samtools sort input.A.splitters.unsorted.bam > input.A.splitters.bam && |
65 samtools sort input.B.splitters.unsorted.bam > input.B.splitters.bam && | 64 samtools sort input.B.splitters.unsorted.bam > input.B.splitters.bam && |
66 samtools view -r readgroup input.A.bam | 65 samtools view input.A.bam |
67 |tail -n +1 | 66 |tail -n +1 |
68 |python $__tool_directory__/pairend_distro.py -r 101 -X 4 -N $seq_method.additional_params.samplingValue -o input.A.lib.histo > meandevA.txt && | 67 |python $__tool_directory__/pairend_distro.py -r $readLength -X 4 -N $seq_method.additional_params.samplingValue -o input.A.lib.histo > meandevA.txt && |
69 samtools view -r readgroup input.B.bam | 68 samtools view input.B.bam |
70 |tail -n +1 | 69 |tail -n +1 |
71 |python $__tool_directory__/pairend_distro.py -r 101 -X 4 -N $seq_method.additional_params.samplingValue -o input.B.lib.histo > meandevB.txt && | 70 |python $__tool_directory__/pairend_distro.py -r $readLengthB -X 4 -N $seq_method.additional_params.samplingValue -o input.B.lib.histo > meandevB.txt && |
72 meanA=\$(cat meandevA.txt | sed s/mean:// | sed -r s/stdev:.+//) && | 71 meanA=\$(cat meandevA.txt | sed s/mean:// | sed -r s/stdev:.+//) && |
73 meanB=\$(cat meandevB.txt | sed s/mean:// | sed -r s/stdev:.+//) && | 72 meanB=\$(cat meandevB.txt | sed s/mean:// | sed -r s/stdev:.+//) && |
74 stdevA=\$(cat meandevA.txt | sed -r s/mean:.+stdev://) && | 73 stdevA=\$(cat meandevA.txt | sed -r s/mean:.+stdev://) && |
75 stdevB=\$(cat meandevB.txt | sed -r s/mean:.+stdev://) && | 74 stdevB=\$(cat meandevB.txt | sed -r s/mean:.+stdev://) && |
76 lumpy -mw $seq_method.additional_params.mw -tt $seq_method.additional_params.tt | 75 <<<<<<< HEAD |
77 #if $output_format == "BEDPE": | 76 lumpy -mw $seq_method.additional_params.mw -tt $seq_method.additional_params.tt |
78 -b | 77 #if $output_format == "BEDPE": |
79 #end if | 78 -b |
80 -pe id:inputA.bam,bam_file:input.A.discordants.bam,histo_file:input.A.lib.histo,mean:"\$meanA",stdev:"\$stdevA",read_length:$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:$seq_method.additional_params.min_mapping_threshold | 79 #end if |
81 -pe id:inputB.bam,bam_file:input.B.discordants.bam,histo_file:input.B.lib.histo,mean:"\$meanB",stdev:"\$stdevA",read_length:$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:$seq_method.additional_params.min_mapping_threshold | 80 -pe id:inputA.bam,bam_file:input.A.discordants.bam,histo_file:input.A.lib.histo,mean:"\$meanA",stdev:"\$stdevA",read_length:$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:$seq_method.additional_params.min_mapping_threshold |
81 -pe id:inputB.bam,bam_file:input.B.discordants.bam,histo_file:input.B.lib.histo,mean:"\$meanB",stdev:"\$stdevA",read_length:$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:$seq_method.additional_params.min_mapping_threshold | |
82 -sr id:inputA.bam,bam_file:input.A.splitters.bam,back_distance:$seq_method.additional_params.back_distance,weight:$seq_method.additional_params.weight,min_mapping_threshold:$seq_method.additional_params.min_mapping_threshold | 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:$seq_method.additional_params.min_mapping_threshold |
83 -sr id:inputB.bam,bam_file:input.B.splitters.bam,back_distance:$seq_method.additional_params.back_distance,weight:$seq_method.additional_params.weight,min_mapping_threshold:$seq_method.additional_params.min_mapping_threshold > output.vcf && | 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 && |
84 mv input.A.discordants.bam $discordants && | 84 mv input.A.discordants.bam $discordants && |
85 mv input.B.discordants.bam $discordantsB && | 85 mv input.B.discordants.bam $discordantsB && |
86 mv input.A.splitters.bam $splits && | 86 mv input.A.splitters.bam $splits && |
102 mv input.A.splitters.unsorted.bam $splits && | 102 mv input.A.splitters.unsorted.bam $splits && |
103 mv input.B.splitters.unsorted.bam $splitsB && | 103 mv input.B.splitters.unsorted.bam $splitsB && |
104 mv output.vcf $vcf_call | 104 mv output.vcf $vcf_call |
105 #end if | 105 #end if |
106 | 106 |
107 | 107 |
108 #end if | 108 #end if |
109 | 109 |
110 ]]></command> | 110 ]]></command> |
111 <!-- basic error handling --> | 111 <!-- basic error handling --> |
112 <inputs> | 112 <inputs> |
150 <param name="back_distance" value="10" type="integer" label="back_distance" help="e.g. 10" /> | 150 <param name="back_distance" value="10" type="integer" label="back_distance" help="e.g. 10" /> |
151 <param name="weight" value="1" type="integer" label="weight" help="e.g. 1" /> | 151 <param name="weight" value="1" type="integer" label="weight" help="e.g. 1" /> |
152 <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" /> |
153 </section> | 153 </section> |
154 </when> | 154 </when> |
155 | 155 |
156 </conditional> | 156 </conditional> |
157 <param help="get variant calling in vcf or BEDPE format" label="variant calling format" name="output_format" type="select"> | 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> | 158 <option selected="True" value="vcf">vcf</option> |
159 <option value="BEDPE">BEDPE</option> | 159 <option value="BEDPE">BEDPE</option> |
160 </param> | 160 </param> |
199 <output name="vcf_call" file="output.vcf" ftype="vcf"/> | 199 <output name="vcf_call" file="output.vcf" ftype="vcf"/> |
200 </test> | 200 </test> |
201 </tests> | 201 </tests> |
202 | 202 |
203 <help> | 203 <help> |
204 | 204 |
205 **Input(s)** | 205 **Input(s)** |
206 | 206 |
207 *One sample* : lumpy search structural variations inside a single sequencing dataset | 207 *One sample* : lumpy search structural variations inside a single sequencing dataset |
208 | 208 |
209 *Two samples*: lumpy search structural variations inside and across two sequencing datasets from two samples | 209 *Two samples*: lumpy search structural variations inside and across two sequencing datasets from two samples |
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 | 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 |
220 | 220 |
221 *Read length*: The length of the sequencing reads in the library. This information is required only for paired-end sequencing data | 221 *Read length*: The length of the sequencing reads in the library. This information is required only for paired-end sequencing data |
222 | 222 |
223 *Additional options*: refer to lumpy-sv_ documentation and the publication (doi 10.1186/gb-2014-15-6-r84) | 223 *Additional options*: refer to lumpy-sv_ documentation and the publication (doi 10.1186/gb-2014-15-6-r84) |
224 | 224 |
225 **lumpy-sv manual** | 225 **lumpy-sv manual** |
226 | 226 |
227 Read the lumpy-sv_ documentation for details on using lumpy. | 227 Read the lumpy-sv_ documentation for details on using lumpy. |
228 | 228 |
229 .. _lumpy-sv: https://github.com/arq5x/lumpy-sv | 229 .. _lumpy-sv: https://github.com/arq5x/lumpy-sv |
269 weight:<sample weight>, | 269 weight:<sample weight>, |
270 read_group:<string> | 270 read_group:<string> |
271 | 271 |
272 -bedpe bedpe_file:<bedpe file>, | 272 -bedpe bedpe_file:<bedpe file>, |
273 id:<sample name>, | 273 id:<sample name>, |
274 weight:<sample weight> | 274 weight:<sample weight> |
275 ]]> | 275 ]]> |
276 </help> | 276 </help> |
277 | 277 |
278 <citations> | 278 <citations> |
279 <citation type="doi">10.1186/gb-2014-15-6-r84</citation> | 279 <citation type="doi">10.1186/gb-2014-15-6-r84</citation> |
280 </citations> | 280 </citations> |