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annotate freebayes.xml @ 27:9f164587a92f draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit d2f9b1728a6525b599e2c014a183b0415b27a870
author iuc
date Tue, 06 Jun 2017 11:44:38 -0400
parents a028d13cd860
children 977a5301b66d
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9f164587a92f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit d2f9b1728a6525b599e2c014a183b0415b27a870
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1 <tool id="freebayes" name="FreeBayes" version="@DEPENDENCY_VERSION@-0">
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2 <description>bayesian genetic variant detector</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <requirements>
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7 <requirement type="package" version="@DEPENDENCY_VERSION@">freebayes</requirement>
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8 <requirement type="package" version="0.1.19">samtools</requirement>
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9 <requirement type="package" version="4.1.3">gawk</requirement>
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10 <requirement type="package" version="20160622">parallel</requirement>
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11 </requirements>
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12 <stdio>
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13 <exit_code range="1:" />
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14 </stdio>
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15 <command><![CDATA[
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16 ##set up input files
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17
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18 #set $reference_fasta_filename = "localref.fa"
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19
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20 #if str( $reference_source.reference_source_selector ) == "history":
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21 ln -s -f '${reference_source.ref_file}' '${reference_fasta_filename}' &&
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22 samtools faidx '${reference_fasta_filename}' 2>&1 || echo "Error running samtools faidx for FreeBayes" >&2 &&
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23 #else:
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24 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
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25 #end if
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27 #if $reference_source.batchmode.processmode == 'merge':
9f164587a92f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit d2f9b1728a6525b599e2c014a183b0415b27a870
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28 #set $input_bamfiles = $reference_source.batchmode.input_bams
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29 #else:
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30 #set $input_bamfiles = [ $reference_source.batchmode.input_bams ]
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31 #end if
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33 #for $bam_count, $input_bam in enumerate( $input_bamfiles ):
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34 ln -s -f '${input_bam}' 'b_${bam_count}.bam' &&
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35 ln -s -f '${input_bam.metadata.bam_index}' 'b_${bam_count}.bam.bai' &&
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36 #end for
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38 ## Tabixize optional input_variant_vcf file (for --variant-input option)
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39 #if ( str( $options_type.options_type_selector ) == 'cline' or str( $options_type.options_type_selector ) == 'full' ) and str( $options_type.optional_inputs.optional_inputs_selector ) == 'set' and str( $options_type.optional_inputs.input_variant_type.input_variant_type_selector ) == "provide_vcf":
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40 ln -s -f '${options_type.optional_inputs.input_variant_type.input_variant_vcf}' 'input_variant_vcf.vcf.gz' &&
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41 ln -s -f '${Tabixized_input}' 'input_variant_vcf.vcf.gz.tbi' &&
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42 #end if
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44 ##if user has specified a region or target file, just use instead of calculating a set of unique regions
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46 #if str( $target_limit_type.target_limit_type_selector ) == "limit_by_target_file":
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47 ln -s '${target_limit_type.input_target_bed}' regions_all.bed &&
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48 #elif str( $target_limit_type.target_limit_type_selector ) == "limit_by_region":
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49 printf '${target_limit_type.region_chromosome}\t${target_limit_type.region_start}\t${target_limit_type.region_end}' > regions_all.bed &&
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50 #else
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51 ##divide up the regions in the bam file for efficient processing
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52 #for $bam_count, $input_bam in enumerate( $input_bamfiles ):
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53 samtools view -H b_${bam_count}.bam |
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54 grep "^@SQ" |
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55 cut -f 2- |
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56 awk '{ gsub("^SN:","",$1);
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57 gsub("^LN:","",$2);
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58 print $1"\t0\t"$2; }' >> regions_all.bed &&
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59 #end for
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60 #end if
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61
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62 sort -u regions_all.bed > regions_uniq.bed &&
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63 ## split into even small chunks, this has some disatvantages and will not be used for the moment
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64 ## bedtools makewindows -b regions_uniq.bed -w 10000000 -s 9990000 > regions.bed &&
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66 mkdir vcf_output &&
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67 mkdir failed_alleles &&
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68 mkdir trace &&
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69
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70 ## Finished setting up inputs
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72 for i in `cat regions_uniq.bed | awk '{print $1":"$2".."$3}'`;
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73 do
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74
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75 echo "
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77 ## COMMAND LINE STARTS HERE
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79 freebayes
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81 --region '\$i'
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82
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83 #for $bam_count, $input_bam in enumerate( $input_bamfiles ):
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84 --bam 'b_${bam_count}.bam'
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85 #end for
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86 --fasta-reference '${reference_fasta_filename}'
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87
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88 ## Outputs
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89 --vcf './vcf_output/part_\$i.vcf'
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90
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91 ##advanced options
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92 #if str( $options_type.options_type_selector ) == "simple":
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93 ##do nothing as command like build up to this point is sufficinet for simple diploid calling
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94
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95 #elif str( $options_type.options_type_selector ) == "simple_w_filters":
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96 --standard-filters
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97 --min-coverage '${options_type.min_coverage}'
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98 #elif str( $options_type.options_type_selector ) == "naive":
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99 --haplotype-length 0
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100 --min-alternate-count 1
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101 --min-alternate-fraction 0
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102 --pooled-continuous
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103 --report-monomorphic
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104 #elif str( $options_type.options_type_selector ) == "naive_w_filters":
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105 --haplotype-length 0
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106 --min-alternate-count 1
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107 --min-alternate-fraction 0
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108 --pooled-continuous
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109 --report-monomorphic
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110 --standard-filters
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111 --min-coverage '${options_type.min_coverage}'
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112
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113 ## Command line direct text entry is not allowed at this time for security reasons
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114 #elif str( $options_type.options_type_selector ) == "full":
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115 #if str( $options_type.optional_inputs.optional_inputs_selector ) == 'set':
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116 ${options_type.optional_inputs.report_monomorphic}
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117
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118 #if $options_type.optional_inputs.output_trace_option:
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119 --trace ./trace/part_'\$i'.txt
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120 #end if
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121 #if $options_type.optional_inputs.output_failed_alleles_option:
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122 --failed-alleles ./failed_alleles/part_'\$i'.bed
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123 #end if
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124 #if $options_type.optional_inputs.samples:
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125 --samples '${options_type.optional_inputs.samples}'
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126 #end if
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127 #if $options_type.optional_inputs.populations:
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128 --populations '${options_type.optional_inputs.populations}'
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129 #end if
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130 #if $options_type.optional_inputs.A:
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131 --cnv-map '${options_type.optional_inputs.A}'
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132 #end if
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133 #if str( $options_type.optional_inputs.input_variant_type.input_variant_type_selector ) == "provide_vcf":
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134 --variant-input 'input_variant_vcf.vcf.gz' ## input_variant_vcf.vcf.gz is symlinked to a galaxy-generated dataset in "Tabixize optional input_variant_vcf file" section of the command line above
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135 ${options_type.optional_inputs.input_variant_type.only_use_input_alleles}
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136 #end if
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137 #if $options_type.optional_inputs.haplotype_basis_alleles:
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138 --haplotype-basis-alleles '${options_type.optional_inputs.haplotype_basis_alleles}'
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139 #end if
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140 #if $options_type.optional_inputs.observation_bias:
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141 --observation-bias '${options_type.optional_inputs.observation_bias}'
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142 #end if
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143 #if $options_type.optional_inputs.contamination_estimates:
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144 --contamination-estimates '${options_type.optional_inputs.contamination_estimates}'
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145 #end if
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146 #end if
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147
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148 ## REPORTING
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149 #if str( $options_type.reporting.reporting_selector ) == "set":
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150 --pvar ${options_type.reporting.pvar}
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151 #end if
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152 ## POPULATION MODEL
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153 #if str( $options_type.population_model.population_model_selector ) == "set":
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154 --theta '${options_type.population_model.T}'
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155 --ploidy '${options_type.population_model.P}'
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156 ${options_type.population_model.J}
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157 ${options_type.population_model.K}
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158 #end if
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159
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160 ## REFERENCE ALLELE
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161 #if str( $options_type.reference_allele.reference_allele_selector ) == "set":
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162 ${options_type.reference_allele.Z}
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163 --reference-quality '${options_type.reference_allele.reference_quality}'
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164 #end if
13
2dd40b601766 Uploaded
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165
25
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166 ## ALLELE SCOPE
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167 #if str( $options_type.allele_scope.allele_scope_selector ) == "set":
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168 ${options_type.allele_scope.I}
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169 ${options_type.allele_scope.i}
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170 ${options_type.allele_scope.X}
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171 ${options_type.allele_scope.u}
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172 ${options_type.allele_scope.no_partial_observations}
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173
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174 -n '${options_type.allele_scope.n}'
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175
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176 --haplotype-length '${options_type.allele_scope.haplotype_length}'
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177 --min-repeat-size '${options_type.allele_scope.min_repeat_length}'
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178 --min-repeat-entropy '${options_type.allele_scope.min_repeat_entropy}'
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179 #end if
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180
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181 ## REALIGNMENT
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182 ${options_type.O}
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183
25
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184 ##INPUT FILTERS
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185 #if str( $options_type.input_filters.input_filters_selector ) == "set":
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186 ${options_type.input_filters.use_duplicate_reads}
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187 -m '${options_type.input_filters.m}'
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188 -q '${options_type.input_filters.q}'
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189 -R '${options_type.input_filters.R}'
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190 -Y '${options_type.input_filters.Y}'
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191 -e '${options_type.input_filters.e}'
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192 -F '${options_type.input_filters.F}'
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193 -C '${options_type.input_filters.C}'
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194 -G '${options_type.input_filters.G}'
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195
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196 #if str( $options_type.input_filters.mismatch_filters.mismatch_filters_selector ) == "set":
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197 -Q '${options_type.input_filters.mismatch_filters.Q}'
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198 -U '${options_type.input_filters.mismatch_filters.U}'
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199 -z '${options_type.input_filters.mismatch_filters.z}'
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200
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201 --read-snp-limit '${options_type.input_filters.mismatch_filters.read_snp_limit}'
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202 #end if
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203
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204 --min-coverage '${options_type.input_filters.min_coverage}'
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205 --min-alternate-qsum "${options_type.input_filters.min_alternate_qsum}"
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206 #end if
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207
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208 ## POPULATION AND MAPPABILITY PRIORS
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209 #if str( $options_type.population_mappability_priors.population_mappability_priors_selector ) == "set":
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210 ${options_type.population_mappability_priors.k}
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211 ${options_type.population_mappability_priors.w}
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212 ${options_type.population_mappability_priors.V}
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213 ${options_type.population_mappability_priors.a}
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214 #end if
25
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215
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216 ## GENOTYPE LIKELIHOODS
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217 #if str( $options_type.genotype_likelihoods.genotype_likelihoods_selector ) == "set":
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218 ${$options_type.genotype_likelihoods.experimental_gls}
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219
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220 --base-quality-cap '${$options_type.genotype_likelihoods.base_quality_cap}'
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221 --prob-contamination '${$options_type.genotype_likelihoods.prob_contamination}'
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222 #end if
25
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223
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224 ## ALGORITHMIC FEATURES
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225 #if str( $options_type.algorithmic_features.algorithmic_features_selector ) == "set":
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226 -B '${options_type.algorithmic_features.B}'
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227 -W '${options_type.algorithmic_features.W}'
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228 -D '${options_type.algorithmic_features.D}'
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229
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230 #if str( $options_type.algorithmic_features.genotype_variant_threshold.genotype_variant_threshold_selector ) == "set":
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231 -S '${options_type.algorithmic_features.genotype_variant_threshold.S}'
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232 #end if
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233
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234 ${options_type.algorithmic_features.N}
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235 ${options_type.algorithmic_features.j}
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236 ${options_type.algorithmic_features.H}
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237 ${options_type.algorithmic_features.genotype_qualities}
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238 ${options_type.algorithmic_features.report_genotype_likelihood_max}
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239
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240 --genotyping-max-banddepth '${options_type.algorithmic_features.genotyping_max_banddepth}'
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241 #end if
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242 #end if
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243
25
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244 ";
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245 done > freebayes_commands.sh &&
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246
25
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247 cat freebayes_commands.sh |
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248 parallel --no-notice -j \${GALAXY_SLOTS:-1} &&
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249
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250 ## make VCF header
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251 grep "^#" "./vcf_output/part_\$i.vcf" > header.txt &&
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252
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253 for i in `cat regions_uniq.bed | awk '{print $1":"$2".."$3}'`;
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254 do
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255 ## if this fails then it bails out the script
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256 cat "./vcf_output/part_\$i.vcf" | grep -v "^#" || true
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257 ;
25
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258 done | sort -k1,1 -k2,2n -k5,5 -u | cat header.txt - > '${output_vcf}'
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259
23
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260 #if str( $options_type.options_type_selector ) == "full":
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261 #if str( $options_type.optional_inputs.optional_inputs_selector ) == 'set':
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262 #if $options_type.optional_inputs.output_failed_alleles_option:
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263 &&
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264 for i in `cat regions.bed | awk '{print $1":"$2".."$3}'`;
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265 do
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266 cat "./failed_alleles/part_\$i.bed"
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267 ;
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268 done > '${output_failed_alleles_bed}'
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269 #end if
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270
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271 #if $options_type.optional_inputs.output_trace_option:
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272 &&
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273 for i in `cat regions.bed | awk '{print $1":"$2".."$3}'`;
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274 do
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275 cat './trace/part_\$i.txt'
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276 ;
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277 done > '${output_trace}'
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278 #end if
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279 #end if
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280 #end if
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281 ]]></command>
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282
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283 <inputs>
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284 <conditional name="reference_source">
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285 <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">
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286 <option value="cached">Locally cached</option>
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287 <option value="history">History</option>
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288 </param>
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289 <when value="cached">
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290 <expand macro="input_bam">
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291 <expand macro="validation" />
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292 </expand>
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293 <param name="ref_file" type="select" label="Using reference genome">
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294 <options from_data_table="fasta_indexes" />
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295 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
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296 </param>
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297 </when>
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298 <when value="history"> <!-- FIX ME!!!! -->
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299 <expand macro="input_bam" />
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300 <param name="ref_file" type="data" format="fasta" label="Use the following dataset as the reference sequence"
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301 help="You can upload a FASTA sequence to the history and use it as reference" />
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302 </when>
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303 </conditional>
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304 <conditional name="target_limit_type">
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305 <param name="target_limit_type_selector" type="select" label="Limit variant calling to a set of regions?" help="Sets --targets or --region options">
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306 <option value="do_not_limit" selected="True">Do not limit</option>
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307 <option value="limit_by_target_file">Limit by target file</option>
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308 <option value="limit_by_region">Limit to region</option>
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309 </param>
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310 <when value="do_not_limit" /><!-- Do nothing here -->
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311 <when value="limit_by_target_file">
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312 <param name="input_target_bed" type="data" format="bed" label="Limit analysis to regions in a file (BED-format)." argument="--targets"/>
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313 </when>
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314 <when value="limit_by_region">
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315 <param name="region_chromosome" type="text" label="Region Chromosome" value="" argument="--region"/> <!--only once? -->
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316 <param name="region_start" type="integer" label="Region Start" value="" />
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317 <param name="region_end" type="integer" label="Region End" value="" />
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318 </when>
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319 </conditional>
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320 <conditional name="options_type">
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321 <param name="options_type_selector" type="select" label="Choose parameter selection level"
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322 help="Select how much control over the freebayes run you need" >
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323 <option value="simple" selected="True">1. Simple diploid calling</option>
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324 <option value="simple_w_filters">2. Simple diploid calling with filtering and coverage</option>
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325 <option value="naive">3. Frequency-based pooled calling</option>
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326 <option value="naive_w_filters">4. Frequency-based pooled calling with filtering and coverage</option>
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327 <option value="full">5. Full list of options</option>
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328 </param>
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329 <when value="full">
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330 <conditional name="optional_inputs">
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331 <param name="optional_inputs_selector" type="select" label="Additional inputs"
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332 help="Sets --samples, --populations, --cnv-map, --trace, --failed-alleles, --varinat-input, --only-use-input-alleles, --haplotype-basis-alleles,
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333 --report-all-haplotype-alleles, --report-monomorphic options, --observation-bias, and --contamination-estimates">
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334 <option value="do_not_set" selected="true">Do not provide additional inputs</option>
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335 <option value="set">Provide additional inputs</option>
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336 </param>
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337 <when value="set">
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338 <param name="output_failed_alleles_option" type="boolean" truevalue="--failed-alleles" falsevalue="" checked="False"
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339 label="Write out failed alleles file" argument="--failed-alleles" />
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340 <param name="output_trace_option" type="boolean" truevalue="--trace" falsevalue="" checked="False"
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341 label="Write out algorithm trace file" argument="--trace"/>
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342 <param name="samples" type="data" format="txt" label="Limit analysis to samples listed (one per line) in the FILE" optional="True"
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343 help="default=By default FreeBayes will analyze all samples in its input BAM files" argument="--samples"/>
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344 <param name="populations" type="data" format="txt" label="Populations File" optional="True"
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345 help="Each line of FILE should list a sample and a population which it is part of. The population-based bayesian inference model will
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346 then be partitioned on the basis of the populations. [default=False]"
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347 argument="--populations" />
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348 <param name="A" type="data" format="bed" label="Read a copy number map from the BED file FILE" optional="True"
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349 help="default=copy number is set to as specified by --ploidy. Read a copy number map from the BED file FILE, which has the format:
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350 reference sequence, start, end, sample name, copy number ... for each region in each sample which does not have the default copy number as set by --ploidy."
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351 argument="--cnv-map" />
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352 <conditional name="input_variant_type">
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353 <param name="input_variant_type_selector" type="select" label="Provide variants file">
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354 <option value="do_not_provide" selected="True">Do not provide</option>
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355 <option value="provide_vcf">Provide VCF file</option>
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356 </param>
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357 <when value="do_not_provide" /><!-- Do nothing here -->
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358 <when value="provide_vcf">
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359 <param name="input_variant_vcf" type="data" format="vcf_bgzip" label="Use variants reported in VCF file as input to the algorithm" argument="--variant-input">
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360 <conversion name="Tabixized_input" type="tabix" />
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361 </param>
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362 <param name="only_use_input_alleles" type="boolean" truevalue="--only-use-input-alleles" falsevalue="" checked="False"
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363 label="Only provide variant calls and genotype likelihoods for sites in VCF" argument="--only-use-input-alleles" />
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364 </when>
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365 </conditional>
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366 <param name="haplotype_basis_alleles" type="data" format="vcf" label="Only use variant alleles provided in this input VCF for the construction of complex or haplotype alleles" optional="True"
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367 argument="--haplotype-basis-alleles" />
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368 <param name="report_monomorphic" type="boolean" truevalue="--report-monomorphic" falsevalue="" checked="False"
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369 label="Report even loci which appear to be monomorphic, and report all considered alleles, even those which are not in called genotypes."
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370 argument="--report-monomorphic" />
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371 <param name="observation_bias" optional="True" type="data" format="tabular" label="Load read length-dependent allele observation biases from"
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372 help="The format is [length] [alignment efficiency relative to reference] where the efficiency is 1 if there is no relative observation bias"
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373 argument="--observation-bias" />
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374 <param name="contamination_estimates" optional="True" type="data" format="tabular" label="Upload per-sample estimates of contamination from"
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375 help="The format should be: sample p(read=R|genotype=AR) p(read=A|genotype=AA) Sample '*' can be used to set default contamination estimates."
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376 argument="--contamination-estimates" />
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377 </when>
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378 <when value="do_not_set" /><!-- do nothing -->
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379 </conditional>
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380
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381 <!-- reporting -->
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382 <conditional name="reporting">
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383 <param name="reporting_selector" type="select" label="Reporting options" help="Sets -P --pvar option">
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384 <option value="do_not_set" selected="True">Use defaults</option>
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385 <option value="set">Set reporting options</option>
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386 </param>
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387 <when value="set">
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388 <param name="pvar" type="float" value="0.0" label="Report sites if the probability that there is a polymorphism at the site is greater than"
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389 help="Note that post-filtering is generally recommended over the use of this parameter. [default=0.0]"
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390 argument="--pvar" />
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391 </when>
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392 <when value="do_not_set" /><!-- do nothing -->
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393 </conditional>
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394
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395 <!-- population model -->
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396 <conditional name="population_model">
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397 <param name="population_model_selector" type="select" label="Population model options"
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398 help="Sets --theta, --ploidy, --pooled-discrete, and --pooled-continuous options " >
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399 <option value="do_not_set" selected="true">Use defaults</option>
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400 <option value="set">Set population model options</option>
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401 </param>
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402 <when value="set">
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403 <param name="T" type="float" value="0.001" label="The expected mutation rate or pairwise nucleotide diversity among the population under analysis"
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404 help="This serves as the single parameter to the Ewens Sampling Formula prior model. [default = 0.001]" argument='--theta'/>
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405 <param name="P" type="integer" value="2" label="Set ploidy for the analysis"
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406 help="default=2" argument='--ploidy' />
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407 <param name="J" type="boolean" truevalue="-J" falsevalue="" checked="False" label="Assume that samples result from pooled sequencing"
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408 help="Model pooled samples using discrete genotypes across pools. When using this flag, set --ploidy to the number of alleles in each sample or use the --cnv-map to define per-sample ploidy. [default=False]"
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409 argument="--pooled-discrete"/>
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410 <param name="K" type="boolean" truevalue="-K" falsevalue="" checked="False" label="Output all alleles which pass input filters, regardles of genotyping outcome or model"
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411 help="default=False." argument="--poled-continuous" />
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412 </when>
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413 <when value="do_not_set" /><!-- do nothing -->
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414 </conditional>
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415
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416 <!-- reference allele -->
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417 <conditional name="reference_allele">
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418 <param name="reference_allele_selector" type="select" label="Reference allele options"
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419 help="Sets --use-reference-allele and --reference-quality options.">
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420 <option value="do_not_set" selected="true">Use defaults</option>
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421 <option value="set">Set reference allele options</option>
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422 </param>
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423 <when value="set">
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424 <param name="Z" type="boolean" truevalue="-Z" falsevalue="" checked="False" label="Include the reference allele in the analysis as if it is another sample from the same population"
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425 help="default=False" argument="--use-reference-allele" />
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426 <param name="reference_quality" type="text" value="100,60" label="Assign mapping quality of MQ (100) to the reference allele at each site and base quality of BQ (60)"
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427 help="default=100,60" argument="--reference-quality" />
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428 </when>
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429 <when value="do_not_set" /><!-- do nothing -->
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430 </conditional>
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431
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432 <!-- allelic scope -->
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433 <conditional name="allele_scope">
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434 <param name="allele_scope_selector" type="select" label="Allelic scope options"
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435 help="Sets -I, i, -X, -u, -n, --haplotype-length, --min-repeat-size, --min-repeat-entropy, and --no-partial-observations options.">
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436 <option value="do_not_set" selected="true">Use defaults</option>
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437 <option value="set">Set alleic scope options</option>
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diff changeset
438 </param>
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439 <when value="set">
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440 <param name="I" type="boolean" truevalue="-I" falsevalue="" checked="False" label="Ignore SNP alleles"
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441 help="default=False" argument="--no-snps" />
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442 <param name="i" type="boolean" truevalue="-i" falsevalue="" checked="False" label="Ignore indels alleles"
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443 help="default=False" argument="--no-indels" />
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444 <param name="X" type="boolean" truevalue="-X" falsevalue="" checked="False" label="Ignore multi-nucleotide polymorphisms, MNPs"
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445 help="default=False" argument="--no-mnps" />
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446 <param name="u" type="boolean" truevalue="-u" falsevalue="" checked="False" label="Ignore complex events (composites of other classes)."
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447 help="default=False" argument="--no-complex" />
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448 <param name="n" type="integer" value="0" label="How many best SNP alleles to evaluate"
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449 help="Alleles are ranked by the sum of supporting quality scores. Set to 0 to evaluate all. [default=0 (all)]"
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450 argument="--use-best-n-alleles" />
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451 <param name="haplotype_length" type="integer" value="3" label="Allow haplotype calls with contiguous embedded matches of up to (nucleotides)"
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452 help="-E --max-complex-gap --haplotype-length; default=3." />
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453 <param name="min_repeat_length" type="integer" value="5" label="When assembling observations across repeats, require the total repeat length at least this many bp"
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454 help="default=5." argument="--min-repeat-size" />
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455 <param name="min_repeat_entropy" type="integer" value="0" label="To detect interrupted repeats, build across sequence until it has entropy > (bits per bp)"
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456 help="default=0 (off)." argument="--min-repeat-entropy" />
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457 <param name="no_partial_observations" type="boolean" truevalue="--no-partial-observations" falsevalue="" checked="False"
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458 label="Exclude observations which do not fully span the dynamically-determined detection window"
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459 help="default=use all observations, dividing partial support across matching haplotypes when generating haplotypes."
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460 argument="--no-partial-observations" />
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461 </when>
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462 <when value="do_not_set" /><!-- do nothing -->
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463 </conditional>
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464
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465 <!-- indel realignment -->
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466 <param name="O" type="boolean" truevalue="-O" falsevalue="" checked="False" label="Turn off left-alignment of indels"
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467 help="default=False (do left align)." argument="--dont-left-align-indels" />
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468
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diff changeset
469 <!-- input filters -->
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470 <conditional name="input_filters">
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471 <param name="input_filters_selector" type="select" label="Input filters"
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472 help="Sets -4, -m, -q, -R, -Y, -Q, -U, -z, -&#36;, -e, -0, -F, -C, -3, -G, and -&#33; options.">
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473 <option value="do_not_set" selected="true">No input filters (default)</option>
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474 <option value="set">Set input filters</option>
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475 </param>
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476 <when value="set">
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477 <param name="use_duplicate_reads" type="boolean" truevalue="--use-duplicate-reads" falsevalue="" checked="False"
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478 label="Include duplicate-marked alignments in the analysis."
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479 help="default=False (exclude duplicates marked as such in alignments)." argument="--use-duplicate-reads" />
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480 <param name="m" type="integer" value="1" label="Exclude alignments from analysis if they have a mapping quality less than"
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481 help="default=1" argument="--min-mapping-quality" />
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482 <param name="q" type="integer" value="0" label="Exclude alleles from analysis if their supporting base quality less than"
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483 help="default=0" argument="--min-base-quality" />
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484 <param name="R" type="integer" value="0" label="Consider any allele in which the sum of qualities of supporting observations is at least"
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485 help="default=0" argument="--min-supporting-allele-qsum" />
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486 <param name="Y" type="integer" value="0" label="Consider any allele in which and the sum of mapping qualities of supporting reads is at least"
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487 help="default=0" argument="--min-supporting-mapping-qsum" />
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488 <conditional name="mismatch_filters">
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489 <param name="mismatch_filters_selector" type="select" label="Mismatch filters"
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490 help="Sets -Q, -U, -z, and &#36; options">
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491 <option value="do_not_set" selected="true">No mismatch filters (default)</option>
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492 <option value="set">Set mismatch filters</option>
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493 </param>
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494 <when value="set">
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495 <param name="Q" type="integer" value="10"
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496 label="Count mismatches toward -U (option below) if the base quality of the mismatch is >="
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497 help="default=10" argument="--mismatch-base-quality-threshold" />
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498 <param name="U" type="integer" value="1000" optional="True"
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499 label="Exclude reads with more than N mismatches where each mismatch has base quality >= Q (option above)"
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500 help="default=~unbound" argument="--read-mismatch-limit" />
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501 <param name="z" type="float" value="1.0" min="0.0" max="1.0"
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502 label="Exclude reads with more than N [0,1] fraction of mismatches where each mismatch has base quality >= Q (second option above)"
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503 help="default=1.0" argument="--read-max-mismatch-fraction" />
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504 <param name="read_snp_limit" type="integer"
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505 value="1000" label="Exclude reads with more than N base mismatches, ignoring gaps with quality >= Q (third option abobe)"
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506 argument="--read-snp-limit" />
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diff changeset
507 </when>
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508 <when value="do_not_set" /><!-- do nothing -->
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509 </conditional>
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510 <param name="e" type="integer" value="1000" label="Exclude reads with more than this number of separate gaps"
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parents: 24
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511 help="default=~unbounded" argument="--read-snp-limit" />
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512 <param name="standard_filters" type="boolean" truevalue="-0" falsevalue="" checked="False"
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diff changeset
513 label="Use stringent input base and mapping quality filters"
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514 help="default=False. Equivalent to -m 30 -q 20 -R 0 -S 0" argument="--standard-filters"/>
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parents: 22
diff changeset
515 <param name="F" type="float" value="0.2"
25
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parents: 24
diff changeset
516 label="Require at least this fraction of observations supporting an alternate allele within a single individual in the in order to evaluate the position"
bf27106652f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 24
diff changeset
517 help="default=0.2" argument="--min-alternate-fraction" />
23
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parents: 22
diff changeset
518 <param name="C" type="integer" value="2"
25
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iuc
parents: 24
diff changeset
519 label="Require at least this count of observations supporting an alternate allele within a single individual in order to evaluate the position"
bf27106652f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
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parents: 24
diff changeset
520 help="default=2" argument="--min-alternate-count" />
23
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parents: 22
diff changeset
521 <param name="min_alternate_qsum" type="integer" value="0"
25
bf27106652f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 24
diff changeset
522 label="Require at least this sum of quality of observations supporting an alternate allele within a single individual in order to evaluate the position"
bf27106652f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 24
diff changeset
523 help="default=0" argument="--min-alternate-qsum" />
23
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parents: 22
diff changeset
524 <param name="G" type="integer" value="1"
25
bf27106652f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 24
diff changeset
525 label="Require at least this count of observations supporting an alternate allele within the total population in order to use the allele in analysis"
bf27106652f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 24
diff changeset
526 help="default=1" argument="--min-alternate-total" />
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iuc
parents: 24
diff changeset
527 <expand macro="par_min_cov" />
23
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parents: 22
diff changeset
528 </when>
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iuc
parents: 24
diff changeset
529 <when value="do_not_set" /><!-- do nothing -->
23
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parents: 22
diff changeset
530 </conditional>
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iuc
parents: 24
diff changeset
531
23
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parents: 22
diff changeset
532 <!-- population and mappability priors -->
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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parents: 22
diff changeset
533 <conditional name="population_mappability_priors">
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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parents: 22
diff changeset
534 <param name="population_mappability_priors_selector" type="select" label="Population and mappability priors"
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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parents: 22
diff changeset
535 help="Sets -k, -w, -V, and -a options.">
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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parents: 22
diff changeset
536 <option value="do_not_set" selected="true">Use defaults</option>
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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parents: 22
diff changeset
537 <option value="set">Set population and mappability priors</option>
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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parents: 22
diff changeset
538 </param>
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parents: 22
diff changeset
539 <when value="set">
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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parents: 22
diff changeset
540 <param name="k" type="boolean" truevalue="-k" falsevalue="" checked="False" label="No population priors"
25
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iuc
parents: 24
diff changeset
541 help="default=False. Equivalent to --pooled-discrete --hwe-priors-off and removal of Ewens Sampling Formula component of priors."
bf27106652f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 24
diff changeset
542 argument="--no-population-priors" />
23
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parents: 22
diff changeset
543 <param name="w" type="boolean" truevalue="-w" falsevalue="" checked="False"
25
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parents: 24
diff changeset
544 label="Disable estimation of the probability of the combination arising under HWE given the allele frequency as estimated by observation frequency"
bf27106652f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 24
diff changeset
545 help="default=False" argument="--hwe-priors-off" />
23
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devteam
parents: 22
diff changeset
546 <param name="V" type="boolean" truevalue="-V" falsevalue="" checked="False" label="Disable incorporation of prior expectations about observations"
25
bf27106652f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 24
diff changeset
547 help="default=False. Uses read placement probability, strand balance probability, and read position (5&#39;'-3&#39;') probability."
bf27106652f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 24
diff changeset
548 argument="--binomial-obs-priors-off" />
23
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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parents: 22
diff changeset
549 <param name="a" type="boolean" truevalue="-a" falsevalue="" checked="False"
25
bf27106652f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 24
diff changeset
550 label="Disable use of aggregate probability of observation balance between alleles as a component of the priors"
bf27106652f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 24
diff changeset
551 help="default=False"
bf27106652f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 24
diff changeset
552 argument="--allele-balance-priors-off" />
23
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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parents: 22
diff changeset
553 </when>
25
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parents: 24
diff changeset
554 <when value="do_not_set" /><!-- do nothing -->
23
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 22
diff changeset
555 </conditional>
25
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iuc
parents: 24
diff changeset
556
23
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 22
diff changeset
557 <!-- genotype likelihoods -->
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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parents: 22
diff changeset
558 <conditional name="genotype_likelihoods">
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 22
diff changeset
559 <param name="genotype_likelihoods_selector" type="select" label="Genotype likelihood options"
25
bf27106652f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 24
diff changeset
560 help="Sets --base-quality-cap, --experimental-gls, and --prob-contamination options.">
23
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 22
diff changeset
561 <option value="do_not_set" selected="true">Use defaults</option>
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 22
diff changeset
562 <option value="set">Set genotype likelihood options</option>
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 22
diff changeset
563 </param>
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 22
diff changeset
564 <when value="set">
25
bf27106652f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 24
diff changeset
565 <param name="base_quality_cap" type="integer" value="0" label="Limit estimated observation quality by capping base quality at"
bf27106652f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 24
diff changeset
566 argument="--base-quality-cap" />
23
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 22
diff changeset
567 <param name="experimental_gls" type="boolean" truevalue="--experimental-gls" falsevalue="" checked="False"
25
bf27106652f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 24
diff changeset
568 label="Generate genotype likelihoods using 'effective base depth' metric qual = 1-BaseQual * 1-MapQual"
bf27106652f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 24
diff changeset
569 help="Incorporate partial observations. This is the default when contamination estimates are provided. Optimized for diploid samples."
bf27106652f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 24
diff changeset
570 argument="--experimental-gls" />
23
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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parents: 22
diff changeset
571 <param name="prob_contamination" type="float" value="10e-9" label="An estimate of contamination to use for all samples"
25
bf27106652f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 24
diff changeset
572 help="default=10e-9." argument="--prob-contamination" />
23
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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parents: 22
diff changeset
573 </when>
25
bf27106652f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 24
diff changeset
574 <when value="do_not_set" /><!-- do nothing -->
23
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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parents: 22
diff changeset
575 </conditional>
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iuc
parents: 24
diff changeset
576
23
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 22
diff changeset
577 <!-- algorithmic features -->
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parents: 22
diff changeset
578 <conditional name="algorithmic_features">
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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parents: 22
diff changeset
579 <param name="algorithmic_features_selector" type="select" label="Algorithmic features"
25
bf27106652f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 24
diff changeset
580 help="Sets --report-genotypes-likelihood-max, -B, --genotyping-max-banddepth, -W, -N, S, -j, -H, -D, -= options">
23
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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parents: 22
diff changeset
581 <option value="do_not_set" selected="true">Use defaults</option>
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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parents: 22
diff changeset
582 <option value="set">Set algorithmic features</option>
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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parents: 22
diff changeset
583 </param>
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 22
diff changeset
584 <when value="set">
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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parents: 22
diff changeset
585 <param name="report_genotype_likelihood_max" type="boolean" truevalue="--report-genotype-likelihood-max" falsevalue="" checked="False"
25
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iuc
parents: 24
diff changeset
586 label="Report genotypes using the maximum-likelihood estimate provided from genotype likelihoods."
bf27106652f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 24
diff changeset
587 help="default=False" argument="--report-genotype-likelihood-max" />
23
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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parents: 22
diff changeset
588 <param name="B" type="integer" value="1000" label="Iterate no more than N times during genotyping step"
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bf27106652f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 24
diff changeset
589 help="default=1000." argument="--genotyping-max-iterations" />
23
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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parents: 22
diff changeset
590 <param name="genotyping_max_banddepth" type="integer" value="6" label="Integrate no deeper than the Nth best genotype by likelihood when genotyping"
25
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iuc
parents: 24
diff changeset
591 help="default=6" argument="--genotyping-max-banddepth" />
23
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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parents: 22
diff changeset
592 <param name="W" type="text" value="1,3"
25
bf27106652f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 24
diff changeset
593 label="Integrate all genotype combinations in our posterior space which include no more than N (1) samples with their Mth (3) best data likelihood"
bf27106652f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 24
diff changeset
594 help="default=1,3" argument="--posterior-integration-limits" />
23
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devteam
parents: 22
diff changeset
595 <param name="N" type="boolean" truevalue="--exclude-unobserved-genotypes" falsevalue="" checked="False"
25
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iuc
parents: 24
diff changeset
596 label="Skip sample genotypings for which the sample has no supporting reads"
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597 help="default=False" argument="--exclude-unobserved-genotypes" />
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598 <conditional name="genotype_variant_threshold">
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599 <param name="genotype_variant_threshold_selector" type="select"
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600 label="Limit posterior integration" argument="--genotype-variant-threshold">
23
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601 <option value="do_not_set" selected="true">Do not limit posterior integration</option>
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602 <option value="set">Set posterior integration limit</option>
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603 </param>
25
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diff changeset
604 <when value="do_not_set" /><!-- do nothing -->
23
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605 <when value="set">
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606 <param name="S" value="" type="integer"
25
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607 label="Limit posterior integration to samples where the second-best genotype likelihood is no more than log(N) from the highest genotype likelihood for the sample."
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608 help="default=~unbounded" argument="--genotype-variant-threshold" />
23
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609 </when>
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610 </conditional>
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611 <param name="j" type="boolean" truevalue="-j" falsevalue="" checked="False"
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612 label="Use mapping quality of alleles when calculating data likelihoods"
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613 help="default=False" argument="--use-mapping-quality" />
23
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614 <param name="H" type="boolean" truevalue="-H" falsevalue="" checked="False"
25
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diff changeset
615 label="Use a weighted sum of base qualities around an indel, scaled by the distance from the indel"
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616 help="default=use a minimum Base Quality in flanking sequence." argument="--harmonic-indel-quality" />
23
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diff changeset
617 <param name="D" type="float" value="0.9" label="Incorporate non-independence of reads by scaling successive observations by this factor during data likelihood calculations"
25
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618 help="default=0.9." argument="--read-dependence-factor" />
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diff changeset
619 <param name="genotype_qualities" type="boolean" truevalue="--genotype-qualities" falsevalue="" checked="False"
25
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parents: 24
diff changeset
620 label="Calculate the marginal probability of genotypes and report as GQ in each sample field in the VCF output"
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diff changeset
621 help="-= --genotype-qualities; default=False " />
23
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622 </when>
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parents: 24
diff changeset
623 <when value="do_not_set" /><!-- do nothing -->
23
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624 </conditional>
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diff changeset
625 </when>
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parents: 24
diff changeset
626 <when value="simple" /><!-- do nothing -->
23
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diff changeset
627 <when value="simple_w_filters">
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diff changeset
628 <!-- add standard-filters to command line -->
25
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629 <expand macro="par_min_cov" />
23
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diff changeset
630 </when>
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631 <when value="naive">
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diff changeset
632 <!-- do nothing build command line using haplotype-length 0 min-alternate-count 1 min-alternate-fraction 0 pooled-continuous report-monomorphic -->
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diff changeset
633 </when>
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diff changeset
634 <when value="naive_w_filters">
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diff changeset
635 <!-- do nothing build command line using haplotype-length 0 min-alternate-count 1 min-alternate-fraction 0 pooled-continuous report-monomorphic standard-filters-->
25
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diff changeset
636 <expand macro="par_min_cov" />
23
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diff changeset
637 </when>
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diff changeset
638 </conditional>
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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diff changeset
639 </inputs>
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diff changeset
640 <outputs>
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diff changeset
641 <data format="vcf" name="output_vcf" label="${tool.name} on ${on_string} (variants)" />
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diff changeset
642 <data format="bed" name="output_failed_alleles_bed" label="${tool.name} on ${on_string} (failed alleles)">
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diff changeset
643 <filter>( options_type['options_type_selector'] == 'cline' or options_type['options_type_selector'] == 'full' ) and options_type['optional_inputs']['optional_inputs_selector'] == 'set' and options_type['optional_inputs']['output_failed_alleles_option'] is True</filter>
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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diff changeset
644 </data>
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diff changeset
645 <data format="txt" name="output_trace" label="${tool.name} on ${on_string} (trace)">
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diff changeset
646 <filter>( options_type['options_type_selector'] == 'cline' or options_type['options_type_selector'] == 'full' ) and options_type['optional_inputs']['optional_inputs_selector'] == 'set' and options_type['optional_inputs']['output_trace_option'] is True</filter>
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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diff changeset
647 </data>
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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diff changeset
648 </outputs>
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diff changeset
649 <tests>
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diff changeset
650 <test>
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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651 <param name="reference_source_selector" value="history" />
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parents: 26
diff changeset
652 <param name="processmode" value="individual" />
23
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653 <param name="ref_file" ftype="fasta" value="freebayes-phix174.fasta"/>
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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654 <param name="input_bams" ftype="bam" value="freebayes-phix174.bam"/>
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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diff changeset
655 <param name="options_type_selector" value="simple"/>
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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656 <output name="output_vcf" file="freebayes-phix174-test1.vcf" compare="contains"/>
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657 </test>
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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parents: 22
diff changeset
658 <test>
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659 <param name="reference_source_selector" value="history" />
27
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diff changeset
660 <param name="processmode" value="individual" />
23
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661 <param name="ref_file" ftype="fasta" value="freebayes-phix174.fasta"/>
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662 <param name="input_bams" ftype="bam" value="freebayes-phix174.bam"/>
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663 <param name="options_type_selector" value="naive_w_filters"/>
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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diff changeset
664 <param name="min_coverage" value="14"/>
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665 <output name="output_vcf" file="freebayes-phix174-test2.vcf" compare="contains"/>
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666 </test>
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diff changeset
667 <test>
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668 <param name="reference_source_selector" value="history" />
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diff changeset
669 <param name="processmode" value="individual" />
23
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670 <param name="ref_file" ftype="fasta" value="freebayes-phix174.fasta"/>
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671 <param name="input_bams" ftype="bam" value="freebayes-phix174.bam"/>
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672 <param name="options_type_selector" value="naive_w_filters"/>
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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parents: 22
diff changeset
673 <param name="min_coverage" value="14"/>
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674 <output name="output_vcf" file="freebayes-phix174-test3.vcf" compare="contains"/>
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675 </test>
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diff changeset
676 <test>
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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677 <param name="reference_source_selector" value="history" />
27
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parents: 26
diff changeset
678 <param name="processmode" value="individual" />
23
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679 <param name="ref_file" ftype="fasta" value="freebayes-phix174.fasta"/>
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680 <param name="input_bams" ftype="bam" value="freebayes-phix174.bam"/>
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681 <param name="options_type_selector" value="full"/>
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diff changeset
682 <param name="population_model_selector" value="set"/>
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683 <param name="P" value="1"/>
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diff changeset
684 <output name="output_vcf" file="freebayes-phix174-test4.vcf" compare="contains"/>
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diff changeset
685 </test>
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686 </tests>
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687 <help>
13
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parents:
diff changeset
688 **What it does**
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parents:
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689
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parents:
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690 FreeBayes is a Bayesian genetic variant detector designed to find small polymorphisms, specifically SNPs (single-nucleotide polymorphisms), indels (insertions and deletions), MNPs (multi-nucleotide polymorphisms), and complex events (composite insertion and substitution events) smaller than the length of a short-read sequencing alignment.
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parents:
diff changeset
691
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parents:
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692 See https://github.com/ekg/freebayes for details on FreeBayes.
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parents:
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693
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parents:
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694 ------
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parents:
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695
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parents:
diff changeset
696 **Description**
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parents:
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697
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parents:
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698 Privided BAM file(s) and a reference. FreeBayes will provide VCF output on standard out describing SNPs, indels, and complex variants in samples in the input alignments.
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699
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parents:
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700 By default, FreeBayes will consider variants supported by at least 2 observations in a single sample (-C) and also by at least 20% of the reads from a single sample (-F). These settings are suitable to low to high depth sequencing in haploid and diploid samples, but users working with polyploid or pooled samples may wish to adjust them depending on the characteristics of their sequencing data.
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parents:
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701
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702 FreeBayes is capable of calling variant haplotypes shorter than a read length where multiple polymorphisms segregate on the same read. The maximum distance between polymorphisms phased in this way is determined by the --max-complex-gap, which defaults to 3bp. In practice, this can comfortably be set to half the read length.
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parents:
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703
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704 Ploidy may be set to any level (-p), but by default all samples are assumed to be diploid. FreeBayes can model per-sample and per-region variation in copy-number (-A) using a copy-number variation map.
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705
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706 FreeBayes can act as a frequency-based pooled caller and describe variants and haplotypes in terms of observation frequency rather than called genotypes. To do so, use --pooled-continuous and set input filters to a suitable level. Allele observation counts will be described by AO and RO fields in the VCF output.
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parents:
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707
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parents:
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708 -------
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parents:
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709
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parents:
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710 **Galaxy-specific options**
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711
25
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712 Galaxy allows five levels of control over FreeBayes options provided by **Choose parameter selection level** menu option. These are:
13
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713
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714 1. *Simple diploid calling*: The simples possible FreeBayes application. Equvalent of using FreeBayes with only a BAM input and no other parameter options.
25
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715 2. *Simple diploid calling with filtering and coverage*: Same as #1 plus two additional options: -0 (standard filters: --min-mapping-quality 30 --min-base-quality 20 --min-supporting-allele-qsum 0 --genotype-varinat-threshold 0) and --min-coverage.
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716 3. *Frequency-based pooled calling*: This is equivalent to using FreeBayes with the following options: --haplotype-length 0 --min-alternate-count 1 --min-alternate-fraction 0 --pooled-continuous --report-monomorphic. This is the best choice for calling varinats in mixtures such as viral, bacterial, or organellar genomes.
13
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717 4. *Frequency-based pooled calling with filtering and coverage*: Same as #3 but adds -0 and --min-coverage like in #2.
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718 5. *Complete list of all options*: Gives you full control by exposing all FreeBayes options as Galaxy widgets.
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719
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720 -----
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721
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722 **FreeBayes options**
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723
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parents:
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724 .. class:: infomark
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725
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726 Note that each Galaxy parameter widget corresponding to command line flags listed below:
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727
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728 Input and output::
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729
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730 -t --targets FILE
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731 Limit analysis to targets listed in the BED-format FILE.
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732 -r --region chrom:start_position-end_position
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733 Limit analysis to the specified region, 0-base coordinates,
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734 end_position included. Either '-' or '..' maybe used as a separator.
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735 -s --samples FILE
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736 Limit analysis to samples listed (one per line) in the FILE.
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737 By default FreeBayes will analyze all samples in its input
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738 BAM files.
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739 --populations FILE
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740 Each line of FILE should list a sample and a population which
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741 it is part of. The population-based bayesian inference model
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742 will then be partitioned on the basis of the populations.
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743 -A --cnv-map FILE
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744 Read a copy number map from the BED file FILE, which has
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745 the format:
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746 reference sequence, start, end, sample name, copy number
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parents:
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747 ... for each region in each sample which does not have the
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748 default copy number as set by --ploidy.
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749 --trace FILE Output an algorithmic trace to FILE.
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750 --failed-alleles FILE
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parents:
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751 Write a BED file of the analyzed positions which do not
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752 pass --pvar to FILE.
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753 -@ --variant-input VCF
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754 Use variants reported in VCF file as input to the algorithm.
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755 Variants in this file will be treated as putative variants
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756 even if there is not enough support in the data to pass
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757 input filters.
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758 -l --only-use-input-alleles
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759 Only provide variant calls and genotype likelihoods for sites
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760 and alleles which are provided in the VCF input, and provide
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761 output in the VCF for all input alleles, not just those which
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762 have support in the data.
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763 --haplotype-basis-alleles VCF
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764 When specified, only variant alleles provided in this input
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765 VCF will be used for the construction of complex or haplotype
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766 alleles.
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767 --report-all-haplotype-alleles
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768 At sites where genotypes are made over haplotype alleles,
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769 provide information about all alleles in output, not only
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770 those which are called.
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771 --report-monomorphic
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772 Report even loci which appear to be monomorphic, and report all
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773 considered alleles, even those which are not in called genotypes.
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774 Loci which do not have any potential alternates have '.' for ALT.
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775
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776 Reporting::
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777
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778 -P --pvar N Report sites if the probability that there is a polymorphism
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779 at the site is greater than N. default: 0.0. Note that post-
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780 filtering is generally recommended over the use of this parameter.
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781
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782 Population model::
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783
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784 -T --theta N The expected mutation rate or pairwise nucleotide diversity
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785 among the population under analysis. This serves as the
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786 single parameter to the Ewens Sampling Formula prior model
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787 default: 0.001
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788 -p --ploidy N Sets the default ploidy for the analysis to N. default: 2
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789 -J --pooled-discrete
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790 Assume that samples result from pooled sequencing.
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791 Model pooled samples using discrete genotypes across pools.
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792 When using this flag, set --ploidy to the number of
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793 alleles in each sample or use the --cnv-map to define
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794 per-sample ploidy.
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795 -K --pooled-continuous
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796 Output all alleles which pass input filters, regardles of
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797 genotyping outcome or model.
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798
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799 Reference allele::
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800
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801 -Z --use-reference-allele
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802 This flag includes the reference allele in the analysis as
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803 if it is another sample from the same population.
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804 --reference-quality MQ,BQ
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805 Assign mapping quality of MQ to the reference allele at each
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806 site and base quality of BQ. default: 100,60
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807
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808 Allele scope::
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809
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810 -I --no-snps Ignore SNP alleles.
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811 -i --no-indels Ignore insertion and deletion alleles.
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812 -X --no-mnps Ignore multi-nuceotide polymorphisms, MNPs.
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parents:
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813 -u --no-complex Ignore complex events (composites of other classes).
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814 -n --use-best-n-alleles N
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815 Evaluate only the best N SNP alleles, ranked by sum of
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parents:
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816 supporting quality scores. (Set to 0 to use all; default: all)
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817 -E --max-complex-gap N
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818 --haplotype-length N
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819 Allow haplotype calls with contiguous embedded matches of up
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820 to this length. (default: 3)
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821 --min-repeat-size N
13
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822 When assembling observations across repeats, require the total repeat
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823 length at least this many bp. (default: 5)
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824 --min-repeat-entropy N
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825 To detect interrupted repeats, build across sequence until it has
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826 entropy > N bits per bp. (default: 0, off)
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827 --no-partial-observations
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828 Exclude observations which do not fully span the dynamically-determined
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829 detection window. (default, use all observations, dividing partial
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830 support across matching haplotypes when generating haplotypes.)
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831
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832 Indel realignment::
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833
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834 -O --dont-left-align-indels
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parents:
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835 Turn off left-alignment of indels, which is enabled by default.
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836
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837 Input filters::
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838
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839 -4 --use-duplicate-reads
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840 Include duplicate-marked alignments in the analysis.
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841 default: exclude duplicates marked as such in alignments
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842 -m --min-mapping-quality Q
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843 Exclude alignments from analysis if they have a mapping
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844 quality less than Q. default: 1
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845 -q --min-base-quality Q
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846 Exclude alleles from analysis if their supporting base
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847 quality is less than Q. default: 0
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848 -R --min-supporting-allele-qsum Q
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849 Consider any allele in which the sum of qualities of supporting
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850 observations is at least Q. default: 0
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851 -Y --min-supporting-mapping-qsum Q
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852 Consider any allele in which and the sum of mapping qualities of
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853 supporting reads is at least Q. default: 0
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854 -Q --mismatch-base-quality-threshold Q
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parents:
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855 Count mismatches toward --read-mismatch-limit if the base
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parents:
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856 quality of the mismatch is >= Q. default: 10
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parents:
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857 -U --read-mismatch-limit N
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parents:
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858 Exclude reads with more than N mismatches where each mismatch
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parents:
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859 has base quality >= mismatch-base-quality-threshold.
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860 default: ~unbounded
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parents:
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861 -z --read-max-mismatch-fraction N
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parents:
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862 Exclude reads with more than N [0,1] fraction of mismatches where
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parents:
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863 each mismatch has base quality >= mismatch-base-quality-threshold
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parents:
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864 default: 1.0
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parents:
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865 -$ --read-snp-limit N
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parents:
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866 Exclude reads with more than N base mismatches, ignoring gaps
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parents:
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867 with quality >= mismatch-base-quality-threshold.
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parents:
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868 default: ~unbounded
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parents:
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869 -e --read-indel-limit N
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parents:
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870 Exclude reads with more than N separate gaps.
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871 default: ~unbounded
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872 -0 --standard-filters Use stringent input base and mapping quality filters
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873 Equivalent to -m 30 -q 20 -R 0 -S 0
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874 -F --min-alternate-fraction N
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875 Require at least this fraction of observations supporting
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diff changeset
876 an alternate allele within a single individual in the
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877 in order to evaluate the position. default: 0.2
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parents:
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878 -C --min-alternate-count N
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parents:
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879 Require at least this count of observations supporting
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parents:
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880 an alternate allele within a single individual in order
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881 to evaluate the position. default: 2
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882 -3 --min-alternate-qsum N
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parents:
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883 Require at least this sum of quality of observations supporting
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parents:
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884 an alternate allele within a single individual in order
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885 to evaluate the position. default: 0
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parents:
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886 -G --min-alternate-total N
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887 Require at least this count of observations supporting
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parents:
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888 an alternate allele within the total population in order
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parents:
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889 to use the allele in analysis. default: 1
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parents:
diff changeset
890 -! --min-coverage N
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parents:
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891 Require at least this coverage to process a site. default: 0
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parents:
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892
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893 Population priors::
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894
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895 -k --no-population-priors
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896 Equivalent to --pooled-discrete --hwe-priors-off and removal of
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parents:
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897 Ewens Sampling Formula component of priors.
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898
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899 Mappability priors::
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900
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901 -w --hwe-priors-off
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902 Disable estimation of the probability of the combination
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903 arising under HWE given the allele frequency as estimated
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parents:
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904 by observation frequency.
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parents:
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905 -V --binomial-obs-priors-off
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parents:
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906 Disable incorporation of prior expectations about observations.
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907 Uses read placement probability, strand balance probability,
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parents:
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908 and read position (5'-3') probability.
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parents:
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909 -a --allele-balance-priors-off
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910 Disable use of aggregate probability of observation balance between alleles
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911 as a component of the priors.
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parents:
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912
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913 Genotype likelihoods::
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914
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915 --observation-bias FILE
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916 Read length-dependent allele observation biases from FILE.
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917 The format is [length] [alignment efficiency relative to reference]
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918 where the efficiency is 1 if there is no relative observation bias.
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919 --base-quality-cap Q
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920 Limit estimated observation quality by capping base quality at Q.
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parents:
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921 --experimental-gls
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922 Generate genotype likelihoods using 'effective base depth' metric
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923 qual = 1-BaseQual * 1-MapQual. Incorporate partial observations.
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924 This is the default when contamination estimates are provided.
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925 Optimized for diploid samples.
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926 --prob-contamination F
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927 An estimate of contamination to use for all samples. default: 10e-9
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928 --contamination-estimates FILE
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parents:
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929 A file containing per-sample estimates of contamination, such as
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parents:
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930 those generated by VerifyBamID. The format should be:
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931 sample p(read=R|genotype=AR) p(read=A|genotype=AA)
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parents:
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932 Sample '*' can be used to set default contamination estimates.
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933
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934 Algorithmic features::
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935
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936 --report-genotype-likelihood-max
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937 Report genotypes using the maximum-likelihood estimate provided
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parents:
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938 from genotype likelihoods.
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parents:
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939 -B --genotyping-max-iterations N
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940 Iterate no more than N times during genotyping step. default: 1000.
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parents:
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941 --genotyping-max-banddepth N
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942 Integrate no deeper than the Nth best genotype by likelihood when
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parents:
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943 genotyping. default: 6.
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944 -W --posterior-integration-limits N,M
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945 Integrate all genotype combinations in our posterior space
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946 which include no more than N samples with their Mth best
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947 data likelihood. default: 1,3.
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948 -N --exclude-unobserved-genotypes
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parents:
diff changeset
949 Skip sample genotypings for which the sample has no supporting reads.
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parents:
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950 -S --genotype-variant-threshold N
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parents:
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951 Limit posterior integration to samples where the second-best
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parents:
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952 genotype likelihood is no more than log(N) from the highest
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parents:
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953 genotype likelihood for the sample. default: ~unbounded
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954 -j --use-mapping-quality
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parents:
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955 Use mapping quality of alleles when calculating data likelihoods.
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956 -H --harmonic-indel-quality
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957 Use a weighted sum of base qualities around an indel, scaled by the
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958 distance from the indel. By default use a minimum BQ in flanking sequence.
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959 -D --read-dependence-factor N
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960 Incorporate non-independence of reads by scaling successive
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parents:
diff changeset
961 observations by this factor during data likelihood
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962 calculations. default: 0.9
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963 -= --genotype-qualities
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964 Calculate the marginal probability of genotypes and report as GQ in
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965 each sample field in the VCF output.
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966
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967
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968 ------
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969
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970 **Acknowledgments**
13
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parents:
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971
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972 The initial version of the wrapper was produced by Dan Blankenberg and upgraded by Anton Nekrutenko.
23
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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diff changeset
973 TNG was developed by Bjoern Gruening
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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974 </help>
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parents: 24
diff changeset
975 <expand macro="citations" />
13
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976 </tool>