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1 <tool id="strelka" name="Strelka" version="1.0.14">
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2 <description>
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3 detects somatic SNVs and small indels in tumour/normal pairs
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4 </description>
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5 <macros>
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6 <import>citations.xml</import>
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7 </macros>
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8 <requirements>
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9 <requirement type="set_environment">STRELKA_INSTALL_DIR</requirement>
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10 <requirement type="set_environment">STRELKA_REPOSITORY_DIR</requirement>
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11 </requirements>
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12 <command detect_errors="aggressive">
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13
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14 <!-- LINK BAM INDEX -->
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15 ln -s $normal normal.bam;
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16 ln -s $normal.metadata.bam_index normal.bam.bai;
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17 ln -s $tumour tumour.bam;
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18 ln -s $tumour.metadata.bam_index tumour.bam.bai;
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19
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20 <!-- CREATE CONFIG FILE -->
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21 touch config.ini;
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22 #if #depthfilters == "genome":
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23 echo "isSkipDepthFilters = 0" >> config.ini;
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24 echo "maxInputDepth = 10000" >> config.ini;
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25 echo "depthFilterMultiple = 3.0" >> config.ini;
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26 #elif #depthfilters == "exome":
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27 echo "isSkipDepthFilters = 1" >> config.ini;
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28 echo "maxInputDepth = 10000" >> config.ini;
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29 echo "depthFilterMultiple = 3.0" >> config.ini;
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30 #elif #depthfilters == "targeted":
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31 echo "isSkipDepthFilters = 1" >> config.ini;
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32 echo "maxInputDepth = 10000" >> config.ini;
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33 echo "depthFilterMultiple = 3.0" >> config.ini;
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34 #else:
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35 echo "isSkipDepthFilters = "$isSkipDepthFilters >> config.ini;
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36 echo "maxInputDepth = "$maxInputDepth >> config.ini;
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37 echo "depthFilterMultiple = "$depthFilterMultiple >> config.ini;
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38 #end if
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39 echo "snvMaxFilteredBasecallFrac = "$advancedsettings.snvMaxFilteredBasecallFrac >> config.ini;
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40 echo "snvMaxSpanningDeletionFrac = "$advancedsettings.snvMaxSpanningDeletionFrac >> config.ini;
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41 echo "indelMaxRefRepeat = "$advancedsettings.indelMaxRefRepeat >> config.ini;
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42 echo "indelMaxWindowFilteredBasecallFrac = "$advancedsettings.indelMaxWindowFilteredBasecallFrac >> config.ini;
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43 echo "indelMaxIntHpolLength = "$advancedsettings.indelMaxIntHpolLength >> config.ini;
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44 echo "ssnvPrior = "$advancedsettings.ssnvPrior >> config.ini;
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45 echo "sindelPrior = "$advancedsettings.sindelPrior >> config.ini;
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46 echo "ssnvNoise = "$advancedsettings.ssnvNoise >> config.ini;
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47 echo "sindelNoise = "$advancedsettings.sindelNoise >> config.ini;
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48 echo "ssnvNoiseStrandBiasFrac = "$advancedsettings.ssnvNoiseStrandBiasFrac >> config.ini;
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49 echo "minTier1Mapq = "$advancedsettings.minTier1Mapq >> config.ini;
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50 echo "minTier2Mapq = "$advancedsettings.minTier2Mapq >> config.ini;
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51 echo "ssnvQuality_LowerBound = "$advancedsettings.ssnvQuality_LowerBound >> config.ini;
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52 echo "sindelQuality_LowerBound = "$advancedsettings.sindelQuality_LowerBound >> config.ini;
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53 echo "isWriteRealignedBam = 0" >> config.ini;
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54 echo "binSize = 25000000" >> config.ini;
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55 echo "extraStrelkaArguments = " >> config.ini;
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56
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57 <!-- INDEX GENOME IF HISTORY -->
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58 #if $reference_source == "history":
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59 ln -s $reference_source.ref_file ref.fa;
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60 samtools faidx ref.fa;
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61 #end if
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62
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63 <!-- CREATE ORIGINAL STRELKA MAKEFILE -->
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64 \$STRELKA_INSTALL_DIR/bin/configureStrelkaWorkflow.pl
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65 --normal \$(pwd)/normal.bam
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66 --tumor \$(pwd)/tumour.bam
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67 #if $reference_source == "history":
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68 --ref ref.fa
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69 #else:
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70 --ref ${reference_source.ref_file.fields.path}
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71 #end if
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72 --config \$(pwd)/config.ini
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73
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74 #if $interval_file
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75
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76 <!-- CREATE SUB-MAKEFILE IF PARALLELISM TURNED ON -->
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77 cp ./strelkaAnalysis/Makefile ./;
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78
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79 \$REPOSITORY_STRELKA_DIR/parse_strelka_makefile.py
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80 --makefile Makefile
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81 --chrom \$(cat $interval_file | cut -f1)
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82 --output ./strelkaAnalysis/Makefile;
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83
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84 #end if
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85
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86 <!-- RUN STRELKA -->
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87 cd strelkaAnalysis;
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88 make -j \${GALAXY_SLOTS:-1};
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89
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90 #if $interval_file
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91
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92 <!-- OUTPUT FOR PARALLEL OPTION - TO BE MERGED -->
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93 cat ./chromosomes/\$(cat $interval_file | cut -f1)/all.somatic.snvs.vcf > $snvs;
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94 cat ./chromosomes/\$(cat $interval_file | cut -f1)/all.somatic.indels.vcf > $indels;
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95
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96 #else
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97
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98 <!-- OUTPUT FOR NORMAL OPTION - ALREADY MERGED -->
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99 cat ./results/all.somatic.snvs.vcf > $snvs;
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100 cat ./results/all.somatic.indels.vcf > $indels;
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101
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102 #end if
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103 </command>
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104 <inputs>
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105 <conditional name="reference_source">
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106 <param label="Choose the source for the reference genome" name="reference_source_selector" type="select">
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107 <option value="cached">Use a built-in genome</option>
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108 <option value="history">Use a genome from the history</option>
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109 </param>
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110 <when value="cached">
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111 <param label="Reference Genome File" name="ref_file" type="select" >
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112 <options from_data_table="fasta_indexes" />
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113 </param>
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114 </when>
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115 <when value="history">
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116 <param label="Reference Genome File" name="ref_file" type="data" format="fasta" />
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117 </when>
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118 </conditional>
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119 <param type="data" format="bam" name="normal" label="Normal Alignment File" />
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120 <param type="data" format="bam" name="tumour" label="Tumour Alignment File" />
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121 <param type="data" format="txt" optional="true" name="interval_file" label="Chromosomes" help="Restrict SNV calls to the following list of chromosomes (one per line)" />
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122 <conditional type="depthfilters">
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123 <param type="select" name="seqType" label="What Type of Sequencing?">
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124 <option value="genome" selected="true">Whole Genome</option>
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125 <option value="exome">Exome</option>
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126 <option value="targeted">Targeted</option>
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127 <option value="other">What are you hiding from me?</option>
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128 </param>
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129 <when value="other">
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130 <param name="isSkipDepthFilters" type="boolean" label="Skip Reads Above Depth Threshold?" help="Should we skip reads if they exist above the chromosome average depth multiplied by the Depth Filter Multiple? Should only be true for Whole Genome Sequencing." checked="true" truevalue="0" falsevalue="1"/>
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131 <param name="depthFilterMultiple" type="float" label="Depth Filter Multiple" value="3.0"/>
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132 <param name="maxInputDepth" type="integer" label="Max Input Depth" value="10000" help="The upper bound on input depth to load into memory. This filter should not occur with Deep Targeted Sequencing but should occur with Exome or Whole Genome Sequencing. Set to 0 to turn off" min="0"/>
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133 </when>
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134 </conditional>
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135 <section name="advancedsettings" title="Advanced Settings" expanded="False">
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136 <param type="float" name="snvMaxFilteredBasecallFrac" value="0.4" label="SNV Max Filtered Basecall Fraction" help="Filter SNV calls when greater than this fraction of basecalls have been removed by a mismatch density filter in either sample."/>
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137 <param type="float" name="snvMaxSpanningDeletionFrac" value="0.75" label="SNV Max Spanning Deletion Fraction" help="Filter SNV calls at sites where greater than this fraction of overlapping reads contain deletions which span the SNV call site."/>
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138 <param type="integer" name="indelMaxRefRepeat" value="8" label="Indel Max Reference Homopolymer Length" help="Filter Indel calls if they represent an expansion or contraction of a repeated pattern with a repeat count greater than this value in the reference."/>
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139 <param type="float" name="indelMaxWindowFilteredBasecallFrac" value="0.3" label="Indel Max Window Filtered Basecall Fraction" help="Filter Indel calls if greater than this fraction of basecalls in a window extending 50 bases to each side of the indel's call positions have been removed by the mismatch density filter."/>
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140 <param type="integer" name="indelMaxIntHpolLength" value="14" label="Indel Max Interrupted Homopolymers Length" help="Filter Indel calls if the longest homopolymer which can be found intersecting or adjacent to the called indel when a single non-homopolymer base is allowed is greater than this length."/>
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141 <param type="float" name="ssnvPrior" value="0.000001" label="SNV Prior Probability"/>
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142 <param type="float" name="sindelPrior" value="0.000001" label="Indel Prior Probability"/>
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143 <param type="float" name="ssnvNoise" value="0.0000005" label="SNV Noise Probability"/>
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144 <param type="float" name="sindelNoise" value="0.000001" label="Indel Noise Probability"/>
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145 <param type="float" name="ssnvNoiseStrandBiasFrac" value="0.5" label="SNV Noise Fraction Attributed to Strand Bias"/>
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146 <param type="integer" name="minTier1Mapq" value="20" label="Min Tier1 Mapping Quality"/>
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147 <param type="integer" name="minTier2Mapq" value="5" label="Min Tier2 Mapping Quality"/>
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148 <param type="integer" name="ssnvQuality_LowerBound" value="15" label="SNV Quality Score Lower Bound"/>
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149 <param type="integer" name="sindelQuality_LowerBound" value="30" label="Indel Quality Score Lower Bound"/>
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150 </section>
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151 </inputs>
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152 <outputs>
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153 <data format="vcf" name="snvs" label="Strelka SNVs"/>
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154 <data format="vcf" name="indels" label="Strelka indels"/>
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155 </outputs>
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156 <tests>
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157 <test>
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158 <param name="normal" value="test.normal.bam"/>
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159 <param name="tumour" value="test.tumour.bam"/>
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160 <param name="reference_source" value="history"/>
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161 <param name="ref_file" value="test.fa"/>
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162 <output name="snvs" ftype="vcf" file="somatic.all.somatic.snvs.vcf" lines_diff="2"/>
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163 <output name="indels" ftype="vcf" file="somatic.all.somatic.indels.vcf" lines_diff="2"/>
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164 </test>
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165 </tests>
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166 <help>
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167
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168 This tool generates VCF files by calling Strelka, a Somatic Nucleotide Variant Caller, on Tumour Normal Pairs.
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169
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170 </help>
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171 <citations>
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172 <expand macro="morinlab_citation"/>
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173 <expand macro="galaxy_citation"/>
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174 <expand macro="strelka_citation"/>
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175 </citations>
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176 </tool>
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