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comparison lumpy.xml @ 0:bbdc52775678 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
author drosofff
date Tue, 06 Dec 2016 05:43:35 -0500
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children aa514338711d
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-1:000000000000 0:bbdc52775678
1 <tool id="lumpy" name="lumpy-sv" version="0.1">
2 <description>find structural variants</description>
3 <requirements>
4 <requirement type="package" version="0.2.12">lumpy-sv</requirement>
5 <requirement type="package" version="1.3.1">samtools</requirement>
6 <requirement type="package" version="1.11.2">numpy</requirement>
7 </requirements>
8 <stdio>
9 <exit_code range="1:" level="fatal" description="Tool exception" />
10 </stdio>
11 <version_command>lumpy --version</version_command>
12 <command><![CDATA[
13 ln -f -s "$input_file" input.bam &&
14 #if $seq_method.seq_method_list == "paired-end":
15 samtools view -b -F 1294 input.bam > "input.discordants.unsorted.bam" &&
16 samtools view -h input.bam | python $__tool_directory__/extractSplitReads_BwaMem.py -i stdin | samtools view -Sb - > "input.splitters.unsorted.bam" &&
17 samtools sort input.discordants.unsorted.bam > input.discordants.bam &&
18 samtools sort input.splitters.unsorted.bam > input.splitters.bam &&
19 samtools view -r readgroup input.bam
20 |tail -n +$seq_method.additional_params.samplingValue
21 |python $__tool_directory__/pairend_distro.py -r 101 -X 4 -N $seq_method.additional_params.samplingValue -o input.lib.histo > meandev.txt &&
22 mean=\$(cat meandev.txt | sed s/mean:// | sed -r s/stdev:.+//) &&
23 stdev=\$(cat meandev.txt | sed -r s/mean:.+stdev://) &&
24 lumpy -mw 4 -tt 0
25 -pe id:input.bam,bam_file:input.discordants.bam,histo_file:input.lib.histo,mean:"\$mean",stdev:"\$stdev",read_length:$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:$seq_method.additional_params.min_mapping_threshold
26 -sr id:input.bam,bam_file:input.splitters.bam,back_distance:$seq_method.additional_params.back_distance,weight:$seq_method.additional_params.weight,min_mapping_threshold:$seq_method.additional_params.min_mapping_threshold > output.vcf &&
27 mv input.discordants.bam $discordants &&
28 mv input.splitters.bam $splits &&
29 mv input.lib.histo $histogram &&
30 mv output.vcf $vcf_call &&
31 rm input.discordants.unsorted.bam input.splitters.unsorted.bam meandev.txt
32 #end if
33 #if $seq_method.seq_method_list == "single-read":
34 samtools view -h input.bam | python $__tool_directory__/extractSplitReads_BwaMem.py -i stdin | samtools view -Sb - > "input.splitters.unsorted.bam" &&
35 lumpy -mw 4 -tt 0
36 -sr id:input.bam,bam_file:input.splitters.unsorted.bam,back_distance:$seq_method.additional_params.back_distance,weight:$seq_method.additional_params.weight,min_mapping_threshold:$seq_method.additional_params.min_mapping_threshold > output.vcf &&
37 mv input.splitters.unsorted.bam $splits &&
38 mv output.vcf $vcf_call
39 #end if
40
41 ]]></command>
42 <!-- basic error handling -->
43 <inputs>
44 <param format="bam" name="input_file" type="data" label="One BAM alignment file produced by BWA-mem"/>
45 <conditional name="seq_method">
46 <param help="Paired-end or single-read sequencing" label="Sequencing method" name="seq_method_list" type="select">
47 <option selected="True" value="paired-end">Paired-end sequencing</option>
48 <option value="single-read">Single-read sequencing</option>
49 </param>
50 <when value="paired-end">
51 <param name="readLength" value="151" type="integer" label="read length" help="e.g. 151 nt" />
52 <section name="additional_params" title="Additional Options" expanded="False">
53 <param name="samplingValue" value="100000" type="integer" label="number of reads to compute mean and stdev of read length" help="e.g. 10000" />
54 <param name="min_non_overlap" value="101" type="integer" label="min_non_overlap" help="e.g. 101" />
55 <param name="discordant_z" value="5" type="integer" label="discordant_z" help="e.g. 5" />
56 <param name="back_distance" value="10" type="integer" label="back_distance" help="e.g. 10" />
57 <param name="weight" value="1" type="integer" label="weight" help="e.g. 1" />
58 <param name="min_mapping_threshold" value="20" type="integer" label="min_mapping_threshold" help="e.g. 20" />
59 </section>
60 </when>
61 <when value="single-read">
62 <section name="additional_params" title="Additional Options" expanded="False">
63 <param name="back_distance" value="10" type="integer" label="back_distance" help="e.g. 10" />
64 <param name="weight" value="1" type="integer" label="weight" help="e.g. 1" />
65 <param name="min_mapping_threshold" value="20" type="integer" label="min_mapping_threshold" help="e.g. 20" />
66 </section>
67 </when>
68
69 </conditional>
70
71 </inputs>
72
73 <outputs>
74 <data format="tabular" name="histogram" type="data" label="${input_file.element_identifier} Fragment size distribution">
75 <filter>seq_method['seq_method_list'] == "paired-end"</filter>
76 </data>
77 <data format="bam" name="splits" type="data" label="${input_file.element_identifier} Split Reads (Bam format)"/>
78 <data format="bam" name="discordants" type="data" label="${input_file.element_identifier} Discordant Pairs (Bam format)">
79 <filter>seq_method['seq_method_list'] == "paired-end"</filter>
80 </data>
81 <data format="vcf" name="vcf_call" type="data" label="${input_file.element_identifier} Variant Calling (vcf format)"/>
82 </outputs>
83
84 <tests>
85 <test>
86 <param name="input_file" value="sr.input.bam" ftype="bam"/>
87 <param name="seq_method_list" value="single-read" />
88 <param name="back_distance" value="10"/>
89 <param name="weight" value="1" />
90 <param name="min_mapping_threshold" value="20" />
91 <output name="vcf_call" file="output.vcf" ftype="vcf"/>
92 </test>
93 </tests>
94
95 <help>
96 Some help required
97 </help>
98
99 <citations>
100 <citation type="doi">10.1186/gb-2014-15-6-r84</citation>
101 </citations>
102 </tool>