Mercurial > repos > mini > strelka
comparison strelka.xml @ 6:87568e5a7d4f
Testing strelka version 0.0.1
| author | mini |
|---|---|
| date | Fri, 26 Sep 2014 13:24:13 +0200 |
| parents | |
| children | 3e8541ece3c7 |
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| 5:07cbbd662111 | 6:87568e5a7d4f |
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| 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> |