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comparison strelka.xml @ 6:87568e5a7d4f

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Testing strelka version 0.0.1
author mini
date Fri, 26 Sep 2014 13:24:13 +0200
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children 3e8541ece3c7
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5:07cbbd662111 6:87568e5a7d4f
1 <tool id="strelka88" name="Strelka good interface but no dependencies">
2
3 <description>Strelka good interface but no dependencies</description>
4 <requirements>
5 <requirement type="package" version="0.1.18">samtools</requirement>
6 <requirement type="package" version="0.1.11">vcftools</requirement>
7 </requirements>
8 <command interpreter="python">strelka_wrapper.py --tumorBam $tumorBam --normalBam $normalBam --refFile $refFile
9 #if $configuration.configuration_switch == 'Default':
10 --configFile Default
11 #else if $configuration.configuration_switch == 'Path':
12 --configFile $configuration.configFile
13 #else:
14 --configFile Custom
15 --depthFilterMultiple $configuration.depthFilterMultiple
16 --snvMaxFilteredBasecallFrac $configuration.snvMaxFilteredBasecallFrac
17 --snvMaxSpanningDeletionFrac $configuration.snvMaxSpanningDeletionFrac
18 --indelMaxRefRepeat $configuration.indelMaxRefRepeat
19 --indelMaxWindowFilteredBasecallFrac $configuration.indelMaxWindowFilteredBasecallFrac
20 --indelMaxIntHpolLength $configuration.indelMaxIntHpolLength
21 --ssnvPrior $configuration.ssnvPrior
22 --sindelPrior $configuration.sindelPrior
23 --ssnvNoise $configuration.ssnvNoise
24 --sindelNoise $configuration.sindelNoise
25 --ssnvNoiseStrandBiasFrac $configuration.ssnvNoiseStrandBiasFrac
26 --minTier1Mapq $configuration.minTier1Mapq
27 --minTier2Mapq $configuration.minTier2Mapq
28 --ssnvQuality_LowerBound $configuration.ssnvQuality_LowerBound
29 --sindelQuality_LowerBound $configuration.sindelQuality_LowerBound
30 --isWriteRealignedBam $configuration.isWriteRealignedBam
31 --binSize $configuration.binSize
32 --isSkipDepthFilters $configuration.isSkipDepthFilters
33 --maxInputDepth $configuration.maxInputDepth
34 #if $configuration.extra_arguments.extra_arguments_switch == 'Yes':
35 --extraStrelkaArguments $configuration.extra_arguments.extraStrelkaArguments
36 #end if
37 #end if
38 </command>
39
40 <inputs>
41 <param format="bam" name="tumorBam" type="data" label="Tumor bam file"/>
42 <param format="bam" name="normalBam" type="data" label="Normal bam file"/>
43 <param format="fasta" name="refFile" type="data" label="ref fasta file"/>
44
45 <conditional name="configuration">
46 <param name="configuration_switch" type="select" label="how do you want to configure strelka">
47 <option value="Default" selected="true">Default</option>
48 <option value="Path">Use a config file</option>
49 <option value="Custom">Custom</option>
50 </param>
51 <when value="Default">
52 <!-- do nothing -->
53 </when>
54 <when value="Path">
55 <param format="ini" name="configFile" type="data" label="config file"/>
56 </when>
57 <when value="Custom">
58 <param name="binSize" type="integer" value="25000000" label="binSize" />
59 <param name="minTier1Mapq" type="integer" value="20" min="0" max="40" help="between 0 and 40" label="minTier1Mapq" />
60 <param name="minTier2Mapq" type="integer" value="5" min="0" max="5" help="between 0 and 5" label="minTier2Mapq" />
61 <param name="isWriteRealignedBam" type="integer" value="0" label="isWriteRealignedBam" />
62 <param name="ssnvPrior" type="float" value="0.000001" label="ssnvPrior" />
63 <param name="sindelPrior" type="float" value="0.000001" label="sindelPrior" />
64 <param name="ssnvNoise" type="float" value="0.0000005" label="ssnvNoise" />
65 <param name="sindelNoise" type="float" value="0.000001" label="sindelNoise" />
66 <param name="ssnvNoiseStrandBiasFrac" type="float" value="0.5" label="ssnvNoiseStrandBiasFrac" />
67 <param name="ssnvQuality_LowerBound" type="integer" value="15" label="ssnvQuality_LowerBound" />
68 <param name="sindelQuality_LowerBound" type="integer" value="30" label="sindelQuality_LowerBound" />
69 <param name="isSkipDepthFilters" type="integer" value="1" label="isSkipDepthFilters" />
70 <param name="depthFilterMultiple" type="float" value="3.0" label="depthFilterMultiple" />
71 <param name="snvMaxFilteredBasecallFrac" type="float" value="0.4" label="snvMaxFilteredBasecallFrac" />
72 <param name="snvMaxSpanningDeletionFrac" type="float" value="0.75" label="snvMaxSpanningDeletionFrac" />
73 <param name="indelMaxRefRepeat" type="integer" value="8" label="indelMaxRefRepeat" />
74 <param name="indelMaxWindowFilteredBasecallFrac" type="float" value="0.3" label="indelMaxWindowFilteredBasecallFrac" />
75 <param name="indelMaxIntHpolLength" type="integer" value="14" label="indelMaxIntHpolLength" />
76 <param name="maxInputDepth" type="integer" value="10000" label="maxInputDepth" />
77 <conditional name="extra_arguments">
78 <param name="extra_arguments_switch" type="select" label="Do you Want to add extraStrelkaArguments?">
79 <option value="No" selected="true">No</option>
80 <option value="Yes">Yes</option>
81 </param>
82 <when value="No">
83 <!-- do nothing -->
84 </when>
85 <when value="Yes">
86 <param name="extraStrelkaArguments" type="text" value="" label="extraStrelkaArguments" />
87 </when>
88 </conditional>
89 </when>
90 </conditional>
91 <conditional name="conf_file">
92 <param name="conf_file_switch" type="select" label="output conf_file ?">
93 <option value="No" selected="true">No</option>
94 <option value="Yes">Yes</option>
95 </param>
96 </conditional>
97
98
99
100
101 </inputs>
102
103 <outputs>
104 <data format="vcf" name="output1_vcf" label="${tool.name} on ${on_string}(passed.somatic.snvs.vcf)" from_work_dir="StrelkaAnalysis/results/passed.somatic.snvs.vcf"/>
105 <data format="vcf" name="output2_vcf" label="${tool.name} on ${on_string}(passed.somatic.indels.vcf)" from_work_dir="StrelkaAnalysis/results/passed.somatic.indels.vcf"/>
106 <data format="vcf" name="output3_vcf" label="${tool.name} on ${on_string}(all.somatic.snvs.vcf)" from_work_dir="StrelkaAnalysis/results/all.somatic.snvs.vcf"/>
107 <data format="vcf" name="output4_vcf" label="${tool.name} on ${on_string}(all.somatic.indels.vcf)" from_work_dir="StrelkaAnalysis/results/all.somatic.indels.vcf"/>
108 <data name="conf_file.ini" label="conf_file.ini" from_work_dir="StrelkaAnalysis/tmp/config.ini">
109 <filter>conf_file.conf_file_switch == "Yes"</filter>
110 </data>
111 </outputs>
112
113 <tests>
114 <test>
115 <param name="normalBam" ftype="bam" value="NA12891_dupmark_chr20_region.bam"/>
116 <param name="tumorBam" ftype="bam" value="NA12892_dupmark_chr20_region.bam"/>
117 <param name="refFile" ftype="fasta" value="chr20_860k_only.fa"/>
118 <param name="configuration_switch" value="Default"/>
119 <output name="output1_vcf" file="passed.somatic.snvs.vcf"/>
120 <output name="output2_vcf" file="passed.somatic.indels.vcf"/>
121 <output name="output3_vcf" file="all.somatic.snvs.vcf"/>
122 <output name="output4_vcf" file="all.somatic.indels.vcf"/>
123 </test>
124 </tests>
125
126 <help>
127 Strelka, a method for somatic SNV and small indel detectipon from sequencing data of matched tumor-normal samples.
128 </help>
129
130 </tool>