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1 <tool id="strelka" name="Strelka">
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2 <!-- Made by Gregoire Seguin-Henry for geviteam in 2014 -->
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3 <description>Strelka</description>
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6
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4 <requirements>
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7
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5 <requirement type="set_environment">SCRIPT_PATH</requirement>
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6
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6 <requirement type="package" version="0.1.18">samtools</requirement>
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7 <requirement type="package" version="0.1.11">vcftools</requirement>
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8 </requirements>
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9 <command interpreter="python">strelka_wrapper.py --tumorBam $tumorBam --normalBam $normalBam --refFile $refFile
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10 #if $configuration.configuration_switch == 'Default':
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11 --configFile Default
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12 #else if $configuration.configuration_switch == 'Path':
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13 --configFile $configuration.configFile
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14 #else:
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15 --configFile Custom
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16 --depthFilterMultiple $configuration.depthFilterMultiple
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17 --snvMaxFilteredBasecallFrac $configuration.snvMaxFilteredBasecallFrac
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18 --snvMaxSpanningDeletionFrac $configuration.snvMaxSpanningDeletionFrac
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19 --indelMaxRefRepeat $configuration.indelMaxRefRepeat
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20 --indelMaxWindowFilteredBasecallFrac $configuration.indelMaxWindowFilteredBasecallFrac
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21 --indelMaxIntHpolLength $configuration.indelMaxIntHpolLength
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22 --ssnvPrior $configuration.ssnvPrior
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23 --sindelPrior $configuration.sindelPrior
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24 --ssnvNoise $configuration.ssnvNoise
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25 --sindelNoise $configuration.sindelNoise
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26 --ssnvNoiseStrandBiasFrac $configuration.ssnvNoiseStrandBiasFrac
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27 --minTier1Mapq $configuration.minTier1Mapq
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28 --minTier2Mapq $configuration.minTier2Mapq
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29 --ssnvQuality_LowerBound $configuration.ssnvQuality_LowerBound
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30 --sindelQuality_LowerBound $configuration.sindelQuality_LowerBound
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31 --isWriteRealignedBam $configuration.isWriteRealignedBam
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32 --binSize $configuration.binSize
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33 --isSkipDepthFilters $configuration.isSkipDepthFilters
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34 --maxInputDepth $configuration.maxInputDepth
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35 #if $configuration.extra_arguments.extra_arguments_switch == 'Yes':
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36 --extraStrelkaArguments $configuration.extra_arguments.extraStrelkaArguments
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37 #end if
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38 #end if
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39 --scriptPath \$SCRIPT_PATH
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40 </command>
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41
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42 <inputs>
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43 <param format="bam" name="tumorBam" type="data" label="Tumor bam file"/>
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44 <param format="bam" name="normalBam" type="data" label="Normal bam file"/>
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45 <param format="fasta" name="refFile" type="data" label="ref fasta file"/>
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46
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47 <conditional name="configuration">
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48 <param name="configuration_switch" type="select" label="how do you want to configure strelka">
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49 <option value="Default" selected="true">Default</option>
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50 <option value="Path">Use a config file</option>
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51 <option value="Custom">Custom</option>
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52 </param>
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53 <when value="Default">
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54 <!-- do nothing -->
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55 </when>
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56 <when value="Path">
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57 <param format="ini" name="configFile" type="data" label="config file"/>
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58 </when>
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59 <when value="Custom">
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60 <param name="binSize" type="integer" value="25000000" label="binSize" />
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61 <param name="minTier1Mapq" type="integer" value="20" min="0" max="40" help="between 0 and 40" label="minTier1Mapq" />
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62 <param name="minTier2Mapq" type="integer" value="5" min="0" max="5" help="between 0 and 5" label="minTier2Mapq" />
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63 <param name="isWriteRealignedBam" type="integer" value="0" min="0" max="1" label="isWriteRealignedBam" help="0 for no alignment else 1"/>
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64 <param name="ssnvPrior" type="float" value="0.000001" label="ssnvPrior" />
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65 <param name="sindelPrior" type="float" value="0.000001" label="sindelPrior" />
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66 <param name="ssnvNoise" type="float" value="0.0000005" label="ssnvNoise" />
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67 <param name="sindelNoise" type="float" value="0.000001" label="sindelNoise" />
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68 <param name="ssnvNoiseStrandBiasFrac" type="float" value="0.5" label="ssnvNoiseStrandBiasFrac" />
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69 <param name="ssnvQuality_LowerBound" type="integer" value="15" label="ssnvQuality_LowerBound" />
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70 <param name="sindelQuality_LowerBound" type="integer" value="30" label="sindelQuality_LowerBound" />
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71 <param name="isSkipDepthFilters" type="integer" value="1" label="isSkipDepthFilters" />
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72 <param name="depthFilterMultiple" type="float" value="3.0" label="depthFilterMultiple" />
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73 <param name="snvMaxFilteredBasecallFrac" type="float" value="0.4" label="snvMaxFilteredBasecallFrac" />
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74 <param name="snvMaxSpanningDeletionFrac" type="float" value="0.75" label="snvMaxSpanningDeletionFrac" />
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75 <param name="indelMaxRefRepeat" type="integer" value="8" label="indelMaxRefRepeat" />
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76 <param name="indelMaxWindowFilteredBasecallFrac" type="float" value="0.3" label="indelMaxWindowFilteredBasecallFrac" />
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77 <param name="indelMaxIntHpolLength" type="integer" value="14" label="indelMaxIntHpolLength" />
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78 <param name="maxInputDepth" type="integer" value="10000" label="maxInputDepth" />
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79 <conditional name="extra_arguments">
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80 <param name="extra_arguments_switch" type="select" label="Do you Want to add extraStrelkaArguments?">
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81 <option value="No" selected="true">No</option>
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82 <option value="Yes">Yes</option>
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83 </param>
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84 <when value="No">
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85 <!-- do nothing -->
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86 </when>
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87 <when value="Yes">
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88 <param name="extraStrelkaArguments" type="text" value="" label="extraStrelkaArguments" />
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89 </when>
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90 </conditional>
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91 </when>
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92 </conditional>
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93 <param name="conf_file_check" type="boolean" label="output conf file" checked="False"/>
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94 <param name="output1_file_check" type="boolean" label="output passed snvs(filtred)" checked="True"/>
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95 <param name="output2_file_check" type="boolean" label="output passed indels(filtred)" checked="True"/>
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96 <param name="output3_file_check" type="boolean" label="output all snvs" checked="True"/>
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97 <param name="output4_file_check" type="boolean" label="output all indels" checked="True"/>
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98 <param name="output5_file_check" type="boolean" label="normal realigned bam" help="only if isWriteRealignedBam option is 1" checked="False"/>
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99 <param name="output6_file_check" type="boolean" label="tumor realigned bam" help="only if isWriteRealignedBam option is 1" checked="False"/>
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100
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101 </inputs>
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102
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103 <outputs>
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104 <data format="vcf" name="output1_vcf" label="${tool.name} on ${on_string}(passed.somatic.snvs.vcf)" from_work_dir="StrelkaAnalysis/results/passed.somatic.snvs.vcf">
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105 <filter>output1_file_check == True</filter>
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106 </data>
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107 <data format="vcf" name="output2_vcf" label="${tool.name} on ${on_string}(passed.somatic.indels.vcf)" from_work_dir="StrelkaAnalysis/results/passed.somatic.indels.vcf">
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108 <filter>output2_file_check == True</filter>
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109 </data>
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110 <data format="vcf" name="output3_vcf" label="${tool.name} on ${on_string}(all.somatic.snvs.vcf)" from_work_dir="StrelkaAnalysis/results/all.somatic.snvs.vcf">
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111 <filter>output3_file_check == True</filter>
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112 </data>
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113 <data format="vcf" name="output4_vcf" label="${tool.name} on ${on_string}(all.somatic.indels.vcf)" from_work_dir="StrelkaAnalysis/results/all.somatic.indels.vcf">
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114 <filter>output4_file_check == True</filter>
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115 </data>
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116 <data name="conf_file.ini" label="conf_file.ini" from_work_dir="StrelkaAnalysis/tmp/config.ini">
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117 <filter>conf_file_check == True</filter>
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118 </data>
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119 <data format="bam" name="output5_bam" label="${tool.name} on ${on_string}(normal.realigned.bam)" from_work_dir="StrelkaAnalysis/realigned/normal.realigned.bam">
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120 <filter>output5_file_check == True</filter>
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121 </data>
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122 <data format="bam" name="output6_bam" label="${tool.name} on ${on_string}(tumor.realigned.bam)" from_work_dir="StrelkaAnalysis/realigned/tumor.realigned.bam">
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123 <filter>output6_file_check == True</filter>
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6
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124 </data>
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125 </outputs>
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126
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127 <tests>
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128 <test>
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129 <param name="normalBam" ftype="bam" value="NA12891_dupmark_chr20_region.bam"/>
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130 <param name="tumorBam" ftype="bam" value="NA12892_dupmark_chr20_region.bam"/>
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131 <param name="refFile" ftype="fasta" value="chr20_860k_only.fa"/>
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132 <param name="configuration_switch" value="Default"/>
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133 <output name="output1_vcf" file="passed.somatic.snvs.vcf"/>
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134 <output name="output2_vcf" file="passed.somatic.indels.vcf"/>
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135 <output name="output3_vcf" file="all.somatic.snvs.vcf"/>
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136 <output name="output4_vcf" file="all.somatic.indels.vcf"/>
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137 </test>
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138 </tests>
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139
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140 <help>
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141 Strelka, a method for somatic SNV and small indel detectipon from sequencing data of matched tumor-normal samples.
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142 </help>
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143
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144 </tool>
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