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annotate freebayes.xml @ 31:57def2d7c093 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 3b5abd63372c2806870627e9dc2a2f0f52f2e52a"
author iuc
date Sat, 27 Nov 2021 09:38:13 +0000
parents ef2c525bd8cd
children 8a7a42541080
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57def2d7c093 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 3b5abd63372c2806870627e9dc2a2f0f52f2e52a"
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1 <tool id="freebayes" name="FreeBayes" version="@TOOL_VERSION@+galaxy1">
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2 <description>bayesian genetic variant detector</description>
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3 <xrefs>
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4 <xref type="bio.tools">freebayes</xref>
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5 </xrefs>
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6 <macros>
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7 <import>macros.xml</import>
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8 </macros>
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9 <expand macro="requirements">
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10 <requirement type="package" version="4.1.3">gawk</requirement>
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11 <requirement type="package" version="20170422">parallel</requirement>
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12 </expand>
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13 <command detect_errors="exit_code"><![CDATA[
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14 ##set up input files
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15
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16 #set $reference_fasta_filename = "localref.fa"
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17
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18 #if str( $reference_source.reference_source_selector ) == "history":
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19 ln -s -f '${reference_source.ref_file}' '${reference_fasta_filename}' &&
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20 samtools faidx '${reference_fasta_filename}' 2>&1 || echo "Error running samtools faidx for FreeBayes" >&2 &&
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21 #else:
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22 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
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23 #end if
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25 #if $reference_source.batchmode.processmode == 'merge':
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26 #set $input_bamfiles = $reference_source.batchmode.input_bams
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27 #else:
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28 #set $input_bamfiles = [ $reference_source.batchmode.input_bams ]
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29 #end if
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31 #for $bam_count, $input_bam in enumerate( $input_bamfiles ):
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32 ln -s -f '${input_bam}' 'b_${bam_count}.bam' &&
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33 ln -s -f '${input_bam.metadata.bam_index}' 'b_${bam_count}.bam.bai' &&
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34 #end for
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35
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36 ## Tabixize optional input_variant_vcf file (for --variant-input option)
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37 #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( $options_type.optional_inputs.input_variant_type.input_variant_type_selector ) == "provide_vcf":
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38 ln -s -f '${options_type.optional_inputs.input_variant_type.input_variant_vcf}' input_variant_vcf.vcf.gz &&
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39 ln -s -f '${Tabixized_input}' input_variant_vcf.vcf.gz.tbi &&
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40 #end if
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41
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42 ##if the user has specified a region or target file, just use that instead of calculating a set of unique regions
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43 #if str( $target_limit_type.target_limit_type_selector ) == "limit_by_target_file":
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44 ln -s '${target_limit_type.input_target_bed}' regions_all.bed &&
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45 #elif str( $target_limit_type.target_limit_type_selector ) == "limit_by_region":
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46 printf '${target_limit_type.region_chromosome}\t${target_limit_type.region_start}\t${target_limit_type.region_end}' > regions_all.bed &&
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47 #else
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48 ##divide up the regions in the bam file for efficient processing
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49 #for $bam_count, $input_bam in enumerate( $input_bamfiles ):
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50 samtools view -H b_${bam_count}.bam |
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51 grep '^@SQ' |
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52 cut -f 2- |
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53 awk '{ gsub("^SN:","",$1); gsub("^LN:","",$2); print $1"\t0\t"$2; }' >> regions_all.bed &&
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54 #end for
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55 #end if
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56
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57 sort -u regions_all.bed > regions_uniq.bed &&
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58 ## split into even small chunks, this has some disatvantages and will not be used for the moment
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59 ## bedtools makewindows -b regions_uniq.bed -w 10000000 -s 9990000 > regions.bed &&
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60
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61 mkdir vcf_output failed_alleles trace &&
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63 ## Finished setting up inputs
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65 for i in `cat regions_uniq.bed | awk '{print $1":"$2".."$3}'`;
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66 do
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67 echo "
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69 ## COMMAND LINE STARTS HERE
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71 freebayes
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72
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73 --region '\$i'
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74
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75 #for $bam_count, $input_bam in enumerate( $input_bamfiles ):
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76 --bam 'b_${bam_count}.bam'
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77 #end for
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78 --fasta-reference '${reference_fasta_filename}'
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79
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80 ## Outputs
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81 --vcf './vcf_output/part_\$i.vcf'
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82
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83 ## Coverage
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84 #if str($coverage_options.coverage_options_selector) == "set":
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85 @COVERAGE@
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86 #end if
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87
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88 ##advanced options
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89 #if str( $options_type.options_type_selector ) == "simple":
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90 #pass
25
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91 #elif str( $options_type.options_type_selector ) == "simple_w_filters":
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92 --standard-filters
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93 #elif str( $options_type.options_type_selector ) == "naive":
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94 --haplotype-length 0
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95 --min-alternate-count 1
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96 --min-alternate-fraction 0.05
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97 --pooled-continuous
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98 --report-monomorphic
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99 #elif str( $options_type.options_type_selector ) == "naive_w_filters":
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100 --haplotype-length 0
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101 --min-alternate-count 1
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102 --min-alternate-fraction 0.05
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103 --pooled-continuous
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104 --report-monomorphic
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105 --standard-filters
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106 #elif str( $options_type.options_type_selector ) == "full":
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107 #if str( $options_type.optional_inputs.optional_inputs_selector ) == 'set':
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108 ${options_type.optional_inputs.report_monomorphic}
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109
25
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110 #if $options_type.optional_inputs.output_trace_option:
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111 --trace ./trace/part_'\$i'.txt
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112 #end if
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113 #if $options_type.optional_inputs.output_failed_alleles_option:
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114 --failed-alleles ./failed_alleles/part_'\$i'.bed
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115 #end if
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116 #if $options_type.optional_inputs.samples:
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117 --samples '${options_type.optional_inputs.samples}'
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118 #end if
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119 #if $options_type.optional_inputs.populations:
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120 --populations '${options_type.optional_inputs.populations}'
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121 #end if
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122 #if $options_type.optional_inputs.A:
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123 --cnv-map '${options_type.optional_inputs.A}'
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124 #end if
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125 #if str( $options_type.optional_inputs.input_variant_type.input_variant_type_selector ) == "provide_vcf":
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126 --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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127 ${options_type.optional_inputs.input_variant_type.only_use_input_alleles}
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128 #end if
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129 #if $options_type.optional_inputs.haplotype_basis_alleles:
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130 --haplotype-basis-alleles '${options_type.optional_inputs.haplotype_basis_alleles}'
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131 #end if
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132 #if $options_type.optional_inputs.observation_bias:
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133 --observation-bias '${options_type.optional_inputs.observation_bias}'
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134 #end if
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135 #if $options_type.optional_inputs.contamination_estimates:
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136 --contamination-estimates '${options_type.optional_inputs.contamination_estimates}'
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137 #end if
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138 #end if
23
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139
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140 ## REPORTING
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141 #if str( $options_type.reporting.reporting_selector ) == "set":
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142 --pvar ${options_type.reporting.pvar}
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143 #end if
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144 ## POPULATION MODEL
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145 #if str( $options_type.population_model.population_model_selector ) == "set":
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146 --theta ${options_type.population_model.T}
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147 --ploidy ${options_type.population_model.P}
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148 ${options_type.population_model.J}
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149 ${options_type.population_model.K}
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150 #end if
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151
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152 ## REFERENCE ALLELE
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153 #if str( $options_type.reference_allele.reference_allele_selector ) == "set":
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154 ${options_type.reference_allele.Z}
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155 --reference-quality '${options_type.reference_allele.reference_quality}'
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156 #end if
13
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157
25
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158 ## ALLELE SCOPE
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159 #if str( $options_type.allele_scope.allele_scope_selector ) == "set":
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160 ${options_type.allele_scope.I}
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161 ${options_type.allele_scope.i}
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162 ${options_type.allele_scope.X}
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163 ${options_type.allele_scope.u}
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164 ${options_type.allele_scope.no_partial_observations}
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165
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166 -n ${options_type.allele_scope.n}
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167
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168 --haplotype-length ${options_type.allele_scope.haplotype_length}
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169 --min-repeat-size ${options_type.allele_scope.min_repeat_length}
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170 --min-repeat-entropy ${options_type.allele_scope.min_repeat_entropy}
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171 #end if
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172
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173 ## REALIGNMENT
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174 ${options_type.O}
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175
25
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176 ##INPUT FILTERS
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177 #if str( $options_type.input_filters.input_filters_selector ) == "set":
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178 $standard_filters
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179 ${options_type.input_filters.use_duplicate_reads}
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180 --min-mapping-quality ${options_type.input_filters.min_mapping_quality}
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181 --min-base-quality ${options_type.input_filters.min_base_quality}
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182 --min-supporting-allele-qsum ${options_type.input_filters.min_supporting_allele_qsum}
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183 --min-supporting-mapping-qsum ${options_type.input_filters.min_supporting_mapping_qsum}
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184 #if str( $options_type.input_filters.mismatch_filters.mismatch_filters_selector ) == "set":
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185 --mismatch-base-quality-threshold ${options_type.input_filters.mismatch_filters.mismatch_base_quality_threshold}
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186 #if str($options_type.input_filters.mismatch_filters.read_mismatch_limit)
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187 --read-mismatch-limit ${options_type.input_filters.mismatch_filters.read_mismatch_limit}
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188 #end if
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189 --read-max-mismatch-fraction ${options_type.input_filters.mismatch_filters.read_max_mismatch_fraction}
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190 --read-snp-limit ${options_type.input_filters.mismatch_filters.read_snp_limit}
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191 #end if
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192 --read-indel-limit ${options_type.input_filters.read_indel_limit}
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193 --min-alternate-fraction ${options_type.input_filters.min_alternate_fraction}
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194 --min-alternate-qsum ${options_type.input_filters.min_alternate_qsum}
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195 --min-alternate-count ${options_type.input_filters.min_alternate_count}
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196 --min-alternate-total ${options_type.input_filters.min_alternate_total}
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197 #end if
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198
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199 ## POPULATION AND MAPPABILITY PRIORS
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200 #if str( $options_type.population_mappability_priors.population_mappability_priors_selector ) == "set":
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201 ${options_type.population_mappability_priors.k}
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202 ${options_type.population_mappability_priors.w}
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203 ${options_type.population_mappability_priors.V}
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204 ${options_type.population_mappability_priors.a}
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205 #end if
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206
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207 ## GENOTYPE LIKELIHOODS
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208 #if str( $options_type.genotype_likelihoods.genotype_likelihoods_selector ) == "set":
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209 ${$options_type.genotype_likelihoods.experimental_gls}
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210
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211 --base-quality-cap ${$options_type.genotype_likelihoods.base_quality_cap}
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212 --prob-contamination ${$options_type.genotype_likelihoods.prob_contamination}
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213 #end if
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214
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215 ## ALGORITHMIC FEATURES
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216 #if str( $options_type.algorithmic_features.algorithmic_features_selector ) == "set":
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217 -B '${options_type.algorithmic_features.B}'
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218 -W '${options_type.algorithmic_features.W}'
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219 -D '${options_type.algorithmic_features.D}'
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220
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221 #if str($options_type.algorithmic_features.genotype_variant_threshold)
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222 -S ${options_type.algorithmic_features.genotype_variant_threshold}
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223 #end if
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224
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225 ${options_type.algorithmic_features.N}
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226 ${options_type.algorithmic_features.j}
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227 ${options_type.algorithmic_features.H}
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228 ${options_type.algorithmic_features.genotype_qualities}
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229 ${options_type.algorithmic_features.report_genotype_likelihood_max}
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230
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231 --genotyping-max-banddepth ${options_type.algorithmic_features.genotyping_max_banddepth}
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232 #end if
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233 #end if
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234
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235 ";
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236 done > freebayes_commands.sh &&
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237
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238 cat freebayes_commands.sh |
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239 parallel --will-cite -j \${GALAXY_SLOTS:-1} &&
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240
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241 ## make VCF header
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242 grep "^#" "./vcf_output/part_\$i.vcf" > header.txt &&
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243
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244 for i in `cat regions_uniq.bed | awk '{print $1":"$2".."$3}'`;
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245 do
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246 ## if this fails then it bails out the script
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247 cat "./vcf_output/part_\$i.vcf" | grep -v "^#" || true
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248 ;
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249 done | sort -k1,1 -k2,2n -k5,5 -u | cat header.txt - > '${output_vcf}'
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250
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251 #if str( $options_type.options_type_selector ) == "full":
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252 #if str( $options_type.optional_inputs.optional_inputs_selector ) == 'set':
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253 #if $options_type.optional_inputs.output_failed_alleles_option:
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254 &&
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255 for i in `cat regions.bed | awk '{print $1":"$2".."$3}'`;
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256 do
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257 cat "./failed_alleles/part_\$i.bed"
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258 ;
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259 done > '${output_failed_alleles_bed}'
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260 #end if
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261
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262 #if $options_type.optional_inputs.output_trace_option:
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263 &&
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264 for i in `cat regions.bed | awk '{print $1":"$2".."$3}'`;
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265 do
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266 cat './trace/part_\$i.txt'
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267 ;
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268 done > '${output_trace}'
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269 #end if
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270 #end if
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271 #end if
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272 ]]></command>
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273
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274 <inputs>
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275 <conditional name="reference_source">
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276 <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">
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277 <option value="cached">Locally cached</option>
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278 <option value="history">History</option>
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279 </param>
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280 <when value="cached">
27
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281 <expand macro="input_bam">
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282 <expand macro="validation" />
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283 </expand>
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284 <param name="ref_file" type="select" label="Using reference genome">
27
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285 <options from_data_table="fasta_indexes" />
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286 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input dataset"/>
23
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287 </param>
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288 </when>
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289 <when value="history"> <!-- FIX ME!!!! -->
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290 <expand macro="input_bam" />
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291 <param name="ref_file" type="data" format="fasta" label="Use the following dataset as the reference sequence"
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292 help="You can upload a FASTA sequence to the history and use it as reference" />
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293 </when>
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294 </conditional>
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295 <conditional name="target_limit_type">
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296 <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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297 <option value="do_not_limit" selected="true">Do not limit</option>
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298 <option value="limit_by_target_file">Limit by target file</option>
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299 <option value="limit_by_region">Limit to region</option>
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300 </param>
28
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301 <when value="do_not_limit" />
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302 <when value="limit_by_target_file">
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303 <param name="input_target_bed" argument="--targets" type="data" format="bed" label="Limit analysis to regions in this BED dataset" />
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304 </when>
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305 <when value="limit_by_region">
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306 <param name="region_chromosome" argument="--region" type="text" label="Region Chromosome" value="" /> <!--only once? -->
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307 <param name="region_start" type="integer" label="Region Start" value="" />
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308 <param name="region_end" type="integer" label="Region End" value="" />
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309 </when>
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310 </conditional>
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311 <conditional name="coverage_options">
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312 <param name="coverage_options_selector" type="select" label="Read coverage"
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313 help="Sets --min-coverage, --limit-coverage, and --skip-coverage">
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314 <option value="do_not_set" selected="true">Use defaults</option>
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315 <option value="set">Specify coverage options</option>
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316 </param>
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317 <when value="set">
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318 <expand macro="par_min_cov" />
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319 </when>
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320 <when value="do_not_set" />
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321 </conditional>
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322 <conditional name="options_type">
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323 <param name="options_type_selector" type="select" label="Choose parameter selection level"
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324 help="Select how much control over the freebayes run you need">
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325 <option value="simple" selected="true">1. Simple diploid calling</option>
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326 <option value="simple_w_filters">2. Simple diploid calling with filtering and coverage</option>
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327 <option value="naive">3. Frequency-based pooled calling</option>
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328 <option value="naive_w_filters">4. Frequency-based pooled calling with filtering and coverage</option>
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329 <option value="full">5. Full list of options</option>
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330 </param>
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331 <when value="full">
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332
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333 <conditional name="optional_inputs">
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334 <param name="optional_inputs_selector" type="select" label="Additional inputs"
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335 help="Sets --samples, --populations, --cnv-map, --trace, --failed-alleles, --variant-input, --only-use-input-alleles, --haplotype-basis-alleles, --report-all-haplotype-alleles, --report-monomorphic options, --observation-bias, and --contamination-estimates">
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336 <option value="do_not_set" selected="true">Do not provide additional inputs</option>
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337 <option value="set">Provide additional inputs</option>
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338 </param>
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339 <when value="set">
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340 <param name="output_failed_alleles_option" argument="--failed-alleles" type="boolean" truevalue="--failed-alleles" falsevalue="" checked="false"
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341 label="Write out failed alleles file" />
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342 <param name="output_trace_option" argument="--trace" type="boolean" truevalue="--trace" falsevalue="" checked="false"
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343 label="Write out algorithm trace file" />
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344 <param argument="--samples" type="data" format="txt"
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345 label="Limit analysis to samples listed (one per line) in this dataset" optional="true"
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346 help="By default FreeBayes will analyze all samples in its input BAM datasets" />
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347 <param argument="--populations" type="data" format="txt" optional="true"
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348 label="Populations dataset"
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349 help="Each line of this dataset should list a sample and a population which it is part of. The population-based bayesian inference model will then be partitioned on the basis of the populations" />
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350 <param name="A" argument="--cnv-map" type="data" format="bed" optional="true"
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351 label="Read a copy number map from a BED dataset"
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352 help="The BED dataset should have the format: '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. If not specified, copy number is set to as specified by --ploidy" />
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353 <conditional name="input_variant_type">
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354 <param name="input_variant_type_selector" type="select" label="Provide variants dataset">
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355 <option value="do_not_provide" selected="true">Do not provide</option>
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356 <option value="provide_vcf">Provide VCF dataset</option>
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357 </param>
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358 <when value="do_not_provide" />
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359 <when value="provide_vcf">
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360 <param name="input_variant_vcf" argument="--variant-input" type="data" format="vcf_bgzip"
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361 label="Use variants reported in this VCF dataset as input to the algorithm">
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362 <conversion name="Tabixized_input" type="tabix" />
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363 </param>
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364 <param name="only_use_input_alleles" argument="--only-use-input-alleles" type="boolean" truevalue="--only-use-input-alleles" falsevalue="" checked="false"
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365 label="Only provide variant calls and genotype likelihoods for sites in VCF" />
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366 </when>
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367 </conditional>
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368 <param name="haplotype_basis_alleles" argument="--haplotype-basis-alleles" type="data" format="vcf" optional="true"
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369 label="Only use variant alleles provided in this input VCF for the construction of complex or haplotype alleles" />
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370 <param name="report_monomorphic" argument="--report-monomorphic" type="boolean" truevalue="--report-monomorphic" falsevalue="" checked="false"
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371 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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372 <param name="observation_bias" argument="--observation-bias" type="data" format="tabular" optional="true"
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373 label="Load read length-dependent allele observation biases from"
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374 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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375 <param name="contamination_estimates" argument="--contamination-estimates" type="data" format="tabular" optional="true"
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376 label="Upload per-sample estimates of contamination from"
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377 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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378 </when>
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379 <when value="do_not_set" />
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380 </conditional>
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381
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382 <!-- reporting -->
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383 <conditional name="reporting">
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384 <param name="reporting_selector" type="select" label="Reporting options" help="Sets -P --pvar option">
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385 <option value="do_not_set" selected="true">Use defaults</option>
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386 <option value="set">Set reporting options</option>
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387 </param>
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388 <when value="set">
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389 <param argument="--pvar" type="float" value="0.0"
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390 label="Report sites if the probability that there is a polymorphism at the site is greater than"
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391 help="Note that post-filtering is generally recommended over the use of this parameter" />
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392 </when>
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393 <when value="do_not_set" />
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394 </conditional>
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395
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396 <!-- population model -->
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397 <conditional name="population_model">
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398 <param name="population_model_selector" type="select" label="Population model options"
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399 help="Sets --theta, --ploidy, --pooled-discrete, and --pooled-continuous options">
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400 <option value="do_not_set" selected="true">Use defaults</option>
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401 <option value="set">Set population model options</option>
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402 </param>
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403 <when value="set">
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404 <param name="T" argument="--theta" type="float" value="0.001"
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405 label="The expected mutation rate or pairwise nucleotide diversity among the population under analysis"
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406 help="This serves as the single parameter to the Ewens Sampling Formula prior model" />
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407 <param name="P" argument="--ploidy" type="integer" value="2"
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408 label="Set ploidy for the analysis" />
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409 <param name="J" argument="--pooled-discrete" type="boolean" truevalue="-J" falsevalue="" checked="false"
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410 label="Assume that samples result from pooled sequencing"
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411 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" />
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412 <param name="K" argument="--poled-continuous" type="boolean" truevalue="-K" falsevalue="" checked="false"
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413 label="Output all alleles which pass input filters, regardles of genotyping outcome or model" />
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414 </when>
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415 <when value="do_not_set" />
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416 </conditional>
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417
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418 <!-- reference allele -->
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419 <conditional name="reference_allele">
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420 <param name="reference_allele_selector" type="select" label="Reference allele options"
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421 help="Sets --use-reference-allele and --reference-quality options">
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422 <option value="do_not_set" selected="true">Use defaults</option>
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423 <option value="set">Set reference allele options</option>
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424 </param>
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425 <when value="set">
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426 <param name="Z" argument="--use-reference-allele" type="boolean" truevalue="-Z" falsevalue="" checked="false"
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427 label="Include the reference allele in the analysis as if it is another sample from the same population" />
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428 <param name="reference_quality" argument="--reference-quality" type="text" value="100,60"
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429 label="Assign mapping quality of MQ (100) to the reference allele at each site and base quality of BQ (60)" />
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430 </when>
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431 <when value="do_not_set" />
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432 </conditional>
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433
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diff changeset
434 <!-- allelic scope -->
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435 <conditional name="allele_scope">
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436 <param name="allele_scope_selector" type="select" label="Allelic scope options"
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437 help="Sets -I, i, -X, -u, -n, --haplotype-length, --min-repeat-size, --min-repeat-entropy, and --no-partial-observations options">
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438 <option value="do_not_set" selected="true">Use defaults</option>
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439 <option value="set">Set alleic scope options</option>
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440 </param>
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441 <when value="set">
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442 <param name="I" argument="--no-snps" type="boolean" truevalue="-I" falsevalue="" checked="false"
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443 label="Ignore SNP alleles" />
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444 <param name="i" argument="--no-indels" type="boolean" truevalue="-i" falsevalue="" checked="false"
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445 label="Ignore indels alleles" />
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parents: 27
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446 <param name="X" argument="--no-mnps" type="boolean" truevalue="-X" falsevalue="" checked="false"
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447 label="Ignore multi-nucleotide polymorphisms, MNPs" />
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448 <param name="u" argument="--no-complex" type="boolean" truevalue="-u" falsevalue="" checked="false"
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449 label="Ignore complex events (composites of other classes)" />
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450 <param name="n" argument="--use-best-n-alleles" type="integer" value="0"
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451 label="How many best SNP alleles to evaluate"
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452 help="Alleles are ranked by the sum of supporting quality scores. Set to 0 to evaluate all" />
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453 <param name="haplotype_length" argument="--haplotype-length" type="integer" value="3"
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454 label="Allow haplotype calls with contiguous embedded matches of up to (nucleotides)" />
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455 <param name="min_repeat_length" argument="--min-repeat-size" type="integer" value="5"
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456 label="When assembling observations across repeats, require the total repeat length at least this many bp" />
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457 <param name="min_repeat_entropy" argument="--min-repeat-entropy" type="integer" value="1"
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458 label="To detect interrupted repeats, build across sequence until it has entropy > (bits per bp)" />
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459 <param name="no_partial_observations" argument="--no-partial-observations" type="boolean" truevalue="--no-partial-observations" falsevalue="" checked="false"
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parents: 24
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460 label="Exclude observations which do not fully span the dynamically-determined detection window"
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461 help="By default, FreeBayes uses all observations, dividing partial support across matching haplotypes when generating haplotypes" />
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462 </when>
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463 <when value="do_not_set" />
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464 </conditional>
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465
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466 <!-- indel realignment -->
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467 <param name="O" argument="--dont-left-align-indels" type="boolean" truevalue="-O" falsevalue="" checked="false"
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468 label="Turn off left-alignment of indels" />
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parents: 24
diff changeset
469
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parents: 22
diff changeset
470 <!-- input filters -->
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471 <conditional name="input_filters">
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472 <param name="input_filters_selector" type="select" label="Input filters">
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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 argument="--standard-filters" type="boolean" truevalue="--standard-filters" falsevalue="" checked="false"
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478 label="Use stringent input base and mapping quality filters"
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479 help="--min-mapping-quality 30 --min-base-quality 20, --min-supporting-allele-qsum 0 --genotype-variant-threshold 0"/>
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480 <param argument="--use-duplicate-reads" type="boolean" truevalue="--use-duplicate-reads" falsevalue="" checked="false"
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481 label="Include duplicate-marked alignments in the analysis" />
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482 <param argument="--min-mapping-quality" type="integer" value="1"
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483 label="Exclude alignments from analysis if they have a mapping quality less than" />
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484 <param argument="--min-base-quality" type="integer" value="0"
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diff changeset
485 label="Exclude alleles from analysis if their supporting base quality less than" />
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486 <param argument="--min-supporting-allele-qsum" type="integer" value="0"
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487 label="Consider any allele in which the sum of qualities of supporting observations is at least" />
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488 <param argument="--min-supporting-mapping-qsum" type="integer" value="0"
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diff changeset
489 label="Consider any allele in which and the sum of mapping qualities of supporting reads is at least" />
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diff changeset
490 <conditional name="mismatch_filters">
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491 <param name="mismatch_filters_selector" type="select" label="Mismatch filters"
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492 help="Sets -Q, -U, -z, and &#36; options">
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493 <option value="do_not_set" selected="true">No mismatch filters (default)</option>
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494 <option value="set">Set mismatch filters</option>
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diff changeset
495 </param>
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496 <when value="set">
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497 <param argument="--mismatch-base-quality-threshold" type="integer" value="10"
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498 label="Count mismatches toward -U (option below) if the base quality of the mismatch is >=" />
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499 <param argument="--read-mismatch-limit" type="integer" value="1000" optional="true"
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500 label="Exclude reads with more than N mismatches where each mismatch has base quality >= mismatch-base-quality-threshold (option above)"
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501 help="default=~unbounded" />
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502 <param argument="--read-max-mismatch-fraction" type="float" value="1.0" min="0.0" max="1.0"
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diff changeset
503 label="Exclude reads with more than N [0,1] fraction of mismatches where each mismatch has base quality >= mismatch-base-quality-threshold (second option above)" />
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504 <param name="read_snp_limit" argument="--read-snp-limit" type="integer" value="1000"
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diff changeset
505 label="Exclude reads with more than N base mismatches, ignoring gaps with quality >= mismatch-base-quality-threshold (third option above)"
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diff changeset
506 help="default=~unbounded" />
23
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diff changeset
507 </when>
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diff changeset
508 <when value="do_not_set" />
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diff changeset
509 </conditional>
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diff changeset
510 <param argument="--read-indel-limit" type="integer" value="1000"
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diff changeset
511 label="Exclude reads with more than this number of separate gaps"
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512 help="default=~unbounded" />
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diff changeset
513 <param argument="--min-alternate-fraction" type="float" value="0.05"
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diff changeset
514 label="Require at least this fraction of observations supporting an alternate allele within a single individual in the in order to evaluate the position" />
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diff changeset
515 <param argument="--min-alternate-qsum" type="integer" value="0"
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diff changeset
516 label="Require at least this sum of quality of observations supporting an alternate allele within a single individual in order to evaluate the position" />
57def2d7c093 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 3b5abd63372c2806870627e9dc2a2f0f52f2e52a"
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diff changeset
517 <param argument="--min-alternate-count" type="integer" value="2"
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diff changeset
518 label="Require at least this count of observations supporting an alternate allele within a single individual in order to evaluate the position" />
31
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diff changeset
519 <param argument="--min-alternate-total" type="integer" value="1"
28
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parents: 27
diff changeset
520 label="Require at least this count of observations supporting an alternate allele within the total population in order to use the allele in analysis" />
23
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parents: 22
diff changeset
521 </when>
28
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diff changeset
522 <when value="do_not_set" />
23
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diff changeset
523 </conditional>
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parents: 24
diff changeset
524
23
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parents: 22
diff changeset
525 <!-- 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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diff changeset
526 <conditional name="population_mappability_priors">
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parents: 22
diff changeset
527 <param name="population_mappability_priors_selector" type="select" label="Population and mappability priors"
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diff changeset
528 help="Sets -k, -w, -V, and -a options">
23
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diff changeset
529 <option value="do_not_set" selected="true">Use defaults</option>
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diff changeset
530 <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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diff changeset
531 </param>
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532 <when value="set">
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parents: 27
diff changeset
533 <param name="k" argument="--no-population-priors" type="boolean" truevalue="-k" falsevalue="" checked="false"
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diff changeset
534 label="No population priors"
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parents: 27
diff changeset
535 help="Equivalent to --pooled-discrete --hwe-priors-off and removal of Ewens Sampling Formula component of priors" />
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parents: 27
diff changeset
536 <param name="w" argument="--hwe-priors-off" type="boolean" truevalue="-w" falsevalue="" checked="false"
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parents: 27
diff changeset
537 label="Disable estimation of the probability of the combination arising under HWE given the allele frequency as estimated by observation frequency" />
977a5301b66d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
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parents: 27
diff changeset
538 <param name="V" argument="--binomial-obs-priors-off" type="boolean" truevalue="-V" falsevalue="" checked="false"
977a5301b66d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
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parents: 27
diff changeset
539 label="Disable incorporation of prior expectations about observations"
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parents: 27
diff changeset
540 help="Uses read placement probability, strand balance probability, and read position (5&#39;'-3&#39;') probability" />
977a5301b66d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
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parents: 27
diff changeset
541 <param name="a" argument="--allele-balance-priors-off" type="boolean" truevalue="-a" falsevalue="" checked="false"
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parents: 27
diff changeset
542 label="Disable use of aggregate probability of observation balance between alleles as a component of the priors" />
23
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diff changeset
543 </when>
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parents: 27
diff changeset
544 <when value="do_not_set" />
23
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parents: 22
diff changeset
545 </conditional>
25
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parents: 24
diff changeset
546
23
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parents: 22
diff changeset
547 <!-- 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
548 <conditional name="genotype_likelihoods">
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parents: 22
diff changeset
549 <param name="genotype_likelihoods_selector" type="select" label="Genotype likelihood options"
28
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parents: 27
diff changeset
550 help="Sets --base-quality-cap, --experimental-gls, and --prob-contamination options">
23
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parents: 22
diff changeset
551 <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
552 <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
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diff changeset
553 </param>
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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diff changeset
554 <when value="set">
28
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parents: 27
diff changeset
555 <param name="base_quality_cap" argument="--base-quality-cap" type="integer" value="0"
977a5301b66d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
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parents: 27
diff changeset
556 label="Limit estimated observation quality by capping base quality at" />
977a5301b66d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
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parents: 27
diff changeset
557 <param name="experimental_gls" argument="--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
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parents: 24
diff changeset
558 label="Generate genotype likelihoods using 'effective base depth' metric qual = 1-BaseQual * 1-MapQual"
28
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iuc
parents: 27
diff changeset
559 help="Incorporate partial observations. This is the default when contamination estimates are provided. Optimized for diploid samples" />
977a5301b66d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 27
diff changeset
560 <param name="prob_contamination" argument="--prob-contamination" type="float" value="10e-9"
977a5301b66d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 27
diff changeset
561 label="An estimate of contamination to use for all samples" />
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
562 </when>
28
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parents: 27
diff changeset
563 <when value="do_not_set" />
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
564 </conditional>
25
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parents: 24
diff changeset
565
23
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parents: 22
diff changeset
566 <!-- 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
567 <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
568 <param name="algorithmic_features_selector" type="select" label="Algorithmic features"
25
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parents: 24
diff changeset
569 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
570 <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
571 <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
572 </param>
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 value="set">
28
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parents: 27
diff changeset
574 <param name="report_genotype_likelihood_max" argument="--report-genotype-likelihood-max" type="boolean" truevalue="--report-genotype-likelihood-max" falsevalue="" checked="false"
977a5301b66d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
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parents: 27
diff changeset
575 label="Report genotypes using the maximum-likelihood estimate provided from genotype likelihoods" />
977a5301b66d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
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parents: 27
diff changeset
576 <param name="B" argument="--genotyping-max-iterations" type="integer" value="1000"
977a5301b66d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
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parents: 27
diff changeset
577 label="Iterate no more than N times during genotyping step" />
977a5301b66d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 27
diff changeset
578 <param name="genotyping_max_banddepth" argument="--genotyping-max-banddepth" type="integer" value="6"
977a5301b66d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
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parents: 27
diff changeset
579 label="Integrate no deeper than the Nth best genotype by likelihood when genotyping" />
977a5301b66d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
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parents: 27
diff changeset
580 <param name="W" argument="--posterior-integration-limits" type="text" value="1,3"
977a5301b66d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
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parents: 27
diff changeset
581 label="Integrate all genotype combinations in our posterior space which include no more than N (1) samples with their Mth (3) best data likelihood" />
977a5301b66d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
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parents: 27
diff changeset
582 <param name="N" argument="--exclude-unobserved-genotypes" type="boolean" truevalue="--exclude-unobserved-genotypes" falsevalue="" checked="false"
977a5301b66d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
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parents: 27
diff changeset
583 label="Skip sample genotypings for which the sample has no supporting reads" />
977a5301b66d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
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parents: 27
diff changeset
584 <param name="genotype_variant_threshold" argument="--genotype-variant-threshold" type="integer" value="" optional="true"
977a5301b66d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 27
diff changeset
585 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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iuc
parents: 27
diff changeset
586 help="default=~unbounded" />
977a5301b66d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
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parents: 27
diff changeset
587 <param name="j" argument="--use-mapping-quality" type="boolean" truevalue="-j" falsevalue="" checked="false"
977a5301b66d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 27
diff changeset
588 label="Use mapping quality of alleles when calculating data likelihoods" />
977a5301b66d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
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parents: 27
diff changeset
589 <param name="H" argument="--harmonic-indel-quality" type="boolean" truevalue="-H" falsevalue="" checked="false"
25
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parents: 24
diff changeset
590 label="Use a weighted sum of base qualities around an indel, scaled by the distance from the indel"
28
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parents: 27
diff changeset
591 help="By default, FreeBayes uses a minimum Base Quality in flanking sequence" />
977a5301b66d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
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parents: 27
diff changeset
592 <param name="D" argument="--read-dependence-factor" type="float" value="0.9"
977a5301b66d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
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parents: 27
diff changeset
593 label="Incorporate non-independence of reads by scaling successive observations by this factor during data likelihood calculations" />
977a5301b66d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 27
diff changeset
594 <param name="genotype_qualities" argument="--genotype-qualities" type="boolean" truevalue="--genotype-qualities" falsevalue="" checked="false"
977a5301b66d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 27
diff changeset
595 label="Calculate the marginal probability of genotypes and report as GQ in each sample field in the VCF output" />
23
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diff changeset
596 </when>
28
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iuc
parents: 27
diff changeset
597 <when value="do_not_set" />
23
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devteam
parents: 22
diff changeset
598 </conditional>
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 22
diff changeset
599 </when>
28
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iuc
parents: 27
diff changeset
600 <when value="simple" />
30
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iuc
parents: 29
diff changeset
601 <when value="simple_w_filters" />
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
602 <when value="naive" />
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
603 <when value="naive_w_filters" />
23
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 22
diff changeset
604 </conditional>
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 22
diff changeset
605 </inputs>
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 22
diff changeset
606 <outputs>
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 22
diff changeset
607 <data format="vcf" name="output_vcf" label="${tool.name} on ${on_string} (variants)" />
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 22
diff changeset
608 <data format="bed" name="output_failed_alleles_bed" label="${tool.name} on ${on_string} (failed alleles)">
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 22
diff changeset
609 <filter>( options_type['options_type_selector'] == 'cline' or options_type['options_type_selector'] == 'full' ) and options_type['optional_inputs']['optional_inputs_selector'] == 'set' and options_type['optional_inputs']['output_failed_alleles_option'] is True</filter>
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 22
diff changeset
610 </data>
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 22
diff changeset
611 <data format="txt" name="output_trace" label="${tool.name} on ${on_string} (trace)">
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 22
diff changeset
612 <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
devteam
parents: 22
diff changeset
613 </data>
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 22
diff changeset
614 </outputs>
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 22
diff changeset
615 <tests>
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 22
diff changeset
616 <test>
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 22
diff changeset
617 <param name="reference_source_selector" value="history" />
27
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iuc
parents: 26
diff changeset
618 <param name="processmode" value="individual" />
23
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 22
diff changeset
619 <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
devteam
parents: 22
diff changeset
620 <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
devteam
parents: 22
diff changeset
621 <param name="options_type_selector" value="simple"/>
29
156b60c1530f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 99e8a87a2993ae644df15756044a40a42aa7a05b
iuc
parents: 28
diff changeset
622 <output name="output_vcf" file="freebayes-phix174-test1.vcf" lines_diff="4" />
23
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 22
diff changeset
623 </test>
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 22
diff changeset
624 <test>
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 22
diff changeset
625 <param name="reference_source_selector" value="history" />
27
9f164587a92f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit d2f9b1728a6525b599e2c014a183b0415b27a870
iuc
parents: 26
diff changeset
626 <param name="processmode" value="individual" />
23
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 22
diff changeset
627 <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
devteam
parents: 22
diff changeset
628 <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
devteam
parents: 22
diff changeset
629 <param name="options_type_selector" value="naive_w_filters"/>
30
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
630 <param name="coverage_options_selector" value="set" />
23
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 22
diff changeset
631 <param name="min_coverage" value="14"/>
29
156b60c1530f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 99e8a87a2993ae644df15756044a40a42aa7a05b
iuc
parents: 28
diff changeset
632 <output name="output_vcf" file="freebayes-phix174-test2.vcf" lines_diff="4" />
23
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 22
diff changeset
633 </test>
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 22
diff changeset
634 <test>
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 22
diff changeset
635 <param name="reference_source_selector" value="history" />
27
9f164587a92f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit d2f9b1728a6525b599e2c014a183b0415b27a870
iuc
parents: 26
diff changeset
636 <param name="processmode" value="individual" />
23
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 22
diff changeset
637 <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
devteam
parents: 22
diff changeset
638 <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
devteam
parents: 22
diff changeset
639 <param name="options_type_selector" value="naive_w_filters"/>
30
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
640 <param name="coverage_options_selector" value="set" />
23
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 22
diff changeset
641 <param name="min_coverage" value="14"/>
29
156b60c1530f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 99e8a87a2993ae644df15756044a40a42aa7a05b
iuc
parents: 28
diff changeset
642 <output name="output_vcf" file="freebayes-phix174-test3.vcf" lines_diff="4" />
23
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 22
diff changeset
643 </test>
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 22
diff changeset
644 <test>
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 22
diff changeset
645 <param name="reference_source_selector" value="history" />
27
9f164587a92f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit d2f9b1728a6525b599e2c014a183b0415b27a870
iuc
parents: 26
diff changeset
646 <param name="processmode" value="individual" />
23
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 22
diff changeset
647 <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
devteam
parents: 22
diff changeset
648 <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
devteam
parents: 22
diff changeset
649 <param name="options_type_selector" value="full"/>
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 22
diff changeset
650 <param name="population_model_selector" value="set"/>
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 22
diff changeset
651 <param name="P" value="1"/>
29
156b60c1530f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 99e8a87a2993ae644df15756044a40a42aa7a05b
iuc
parents: 28
diff changeset
652 <output name="output_vcf" file="freebayes-phix174-test4.vcf" lines_diff="4" />
23
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 22
diff changeset
653 </test>
30
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
654 <test>
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
655 <param name="reference_source_selector" value="history" />
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
656 <param name="processmode" value="individual" />
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
657 <param name="ref_file" ftype="fasta" value="freebayes-hxb2.fasta"/>
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
658 <param name="input_bams" ftype="bam" value="freebayes-hxb2.bam"/>
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
659 <param name="options_type_selector" value="simple"/>
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
660 <param name="coverage_options_selector" value="set" />
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
661 <param name="min_coverage" value="250" />
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
662 <output name="output_vcf" file="freebayes-hxb2-test5.vcf" lines_diff="4" />
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
663 </test>
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
664 <test>
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
665 <param name="reference_source_selector" value="history" />
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
666 <param name="processmode" value="individual" />
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
667 <param name="ref_file" ftype="fasta" value="freebayes-hxb2.fasta"/>
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
668 <param name="input_bams" ftype="bam" value="freebayes-hxb2.bam"/>
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
669 <param name="options_type_selector" value="simple"/>
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
670 <param name="coverage_options_selector" value="set" />
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
671 <param name="limit_coverage" value="400" />
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
672 <output name="output_vcf" file="freebayes-hxb2-test6.vcf" lines_diff="4" />
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
673 </test>
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
674 <test>
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
675 <param name="reference_source_selector" value="history" />
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
676 <param name="processmode" value="individual" />
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
677 <param name="ref_file" ftype="fasta" value="freebayes-hxb2.fasta"/>
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
678 <param name="input_bams" ftype="bam" value="freebayes-hxb2.bam"/>
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679 <param name="options_type_selector" value="simple"/>
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680 <param name="coverage_options_selector" value="set" />
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681 <param name="skip_coverage" value="100" />
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682 <output name="output_vcf" file="freebayes-hxb2-test7.vcf" lines_diff="4" />
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683 </test>
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684 </tests>
30
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685 <help><![CDATA[
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686 **What it does**
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687
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688 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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689
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690 See https://github.com/ekg/freebayes for details on FreeBayes.
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691
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692 ------
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693
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694 **Description**
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695
28
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696 Provided some BAM dataset(s) and a reference sequence, FreeBayes will produce a VCF dataset describing SNPs, indels, and complex variants in samples in the input alignments.
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697
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698 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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699
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700 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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701
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702 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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703
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704 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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705
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706 -------
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707
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708 **Galaxy-specific options**
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709
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710 Galaxy allows five levels of control over FreeBayes options, provided by the **Choose parameter selection level** menu option. These are:
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711
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712 1. *Simple diploid calling*: The simplest possible FreeBayes application. Equivalent to using FreeBayes with only a BAM input and no other parameter options.
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713 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-variant-threshold 0) and --min-coverage.
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714 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 variants in mixtures such as viral, bacterial, or organellar genomes.
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715 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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716 5. *Complete list of all options*: Gives you full control by exposing all FreeBayes options as Galaxy parameters.
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717
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718 ------
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719
30
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720 **Command-line parameters**
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diff changeset
721
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722 **Input**::
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723
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724 --bam FILE The file or set of BAM files to be analyzed.
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725 --bam-list FILE A file containing a list of BAM files to be analyzed.
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726
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727 --stdin Read BAM input on stdin.
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728 --fasta-reference FILE Use FILE as the reference sequence for analysis.
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729 An index file (FILE.fai) will be created if none exists.
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730 If neither --targets nor --region are specified, FreeBayes
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731 will analyze every position in this reference.
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
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732 --targets FILE Limit analysis to targets listed in the BED-format FILE.
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733 --region <chrom>:<start>-<end> Limit analysis to the specified region, 0-base coordinates,
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
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734 end_position not included (same as BED format).
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735 Either '-' or '..' maybe used as a separator.
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
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736 --samples FILE 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 Each line of FILE should list a sample and a population which
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
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740 it is part of. The population-based bayesian inference model
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741 will then be partitioned on the basis of the populations.
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
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742 --cnv-map FILE Read a copy number map from the BED file FILE, which has
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
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743 either a sample-level ploidy:
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
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744 sample_name copy_number
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745 or a region-specific format:
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746 seq_name start end sample_name copy_number
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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. These fields can be delimited
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749 by space or tab.
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750
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751 **Output**::
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752
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753 --vcf FILE Output VCF-format results to FILE. (default: stdout)
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754 --gvcf Write gVCF output, which indicates coverage in uncalled regions.
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755 --gvcf-chunk NUM When writing gVCF output emit a record for every NUM bases.
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756 --gvcf-dont-use-chunk When writing the gVCF output emit a record for all bases if
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
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757 set to "true" , will also route an int to --gvcf-chunk
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758 similar to --output-mode EMIT_ALL_SITES from GATK
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759 --variant-input VCF Use variants reported in VCF file as input to the algorithm.
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760 Variants in this file will included in the output even if
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761 there is not enough support in the data to pass input filters.
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762 --only-use-input-alleles Only provide variant calls and genotype likelihoods for sites
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763 and alleles which are provided in the VCF input, and provide
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
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764 output in the VCF for all input alleles, not just those which
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
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765 have support in the data.
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
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766 --haplotype-basis-alleles VCF When specified, only variant alleles provided in this input
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
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767 VCF will be used for the construction of complex or haplotype
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768 alleles.
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769 --report-all-haplotype-alleles At sites where genotypes are made over haplotype alleles,
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
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770 provide information about all alleles in output, not only
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771 those which are called.
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772 --report-monomorphic 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.
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
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774 Loci which do not have any potential alternates have '.' for ALT.
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diff changeset
775 --pvar N Report sites if the probability that there is a polymorphism
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
776 at the site is greater than N. default: 0.0. Note that post-
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
777 filtering is generally recommended over the use of this parameter.
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
778 --strict-vcf Generate strict VCF format (FORMAT/GQ will be an int)
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
779
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
780 **Population model**::
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
781
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
782 --theta N The expected mutation rate or pairwise nucleotide diversity
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
783 among the population under analysis. This serves as the
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
784 single parameter to the Ewens Sampling Formula prior model
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
785 default: 0.001
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
786 --ploidy N Sets the default ploidy for the analysis to N. default: 2
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
787 --pooled-discrete Assume that samples result from pooled sequencing.
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
788 Model pooled samples using discrete genotypes across pools.
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
789 When using this flag, set --ploidy to the number of
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
790 alleles in each sample or use the --cnv-map to define
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
791 per-sample ploidy.
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
792 --pooled-continuous Output all alleles which pass input filters, regardles of
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
793 genotyping outcome or model.
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
794
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
795 **Reference allele**::
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
796
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
797 --use-reference-allele This flag includes the reference allele in the analysis as
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
798 if it is another sample from the same population.
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
799 --reference-quality MQ,BQ Assign mapping quality of MQ to the reference allele at each
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
800 site and base quality of BQ. default: 100,60
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
801
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
802 **Allele scope**::
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
803
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
804 --use-best-n-alleles N Evaluate only the best N SNP alleles, ranked by sum of
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
805 supporting quality scores. (Set to 0 to use all; default: all)
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
806 --max-complex-gap
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
807 --haplotype-length N Allow haplotype calls with contiguous embedded matches of up
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
808 to this length. Set N=-1 to disable clumping. (default: 3)
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
809 --min-repeat-size When assembling observations across repeats, require the total repeat
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
810 length at least this many bp. (default: 5)
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
811 --min-repeat-entropy N To detect interrupted repeats, build across sequence until it has
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
812 entropy > N bits per bp. Set to 0 to turn off. (default: 1)
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
813 --no-partial-observations Exclude observations which do not fully span the dynamically-determined
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
814 detection window. (default, use all observations, dividing partial
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
815 support across matching haplotypes when generating haplotypes.)
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
816
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
817 **Indel realignment**::
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
818
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
819 --dont-left-align-indels Turn off left-alignment of indels, which is enabled by default.
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
820
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
821 **Input filters**::
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
822
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
823 --use-duplicate-reads Include duplicate-marked alignments in the analysis.
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
824 default: exclude duplicates marked as such in alignments
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
825 --min-mapping-quality Q Exclude alignments from analysis if they have a mapping
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
826 quality less than Q. default: 1
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
827 --min-base-quality Q Exclude alleles from analysis if their supporting base
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
828 quality is less than Q. default: 0
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
829 --min-supporting-allele-qsum Q Consider any allele in which the sum of qualities of supporting
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
830 observations is at least Q. default: 0
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
831 --min-supporting-mapping-qsum Q Consider any allele in which and the sum of mapping qualities of
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
832 supporting reads is at least Q. default: 0
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
833 --mismatch-base-quality-threshold Q Count mismatches toward --read-mismatch-limit if the base
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
834 quality of the mismatch is >= Q. default: 10
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
835 --read-mismatch-limit N Exclude reads with more than N mismatches where each mismatch
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
836 has base quality >= mismatch-base-quality-threshold.
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
837 default: ~unbounded
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
838 --read-max-mismatch-fraction N Exclude reads with more than N [0,1] fraction of mismatches where
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
839 each mismatch has base quality >= mismatch-base-quality-threshold
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
840 default: 1.0
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
841 --read-snp-limit N Exclude reads with more than N base mismatches, ignoring gaps
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
842 with quality >= mismatch-base-quality-threshold.
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
843 default: ~unbounded
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
844 --read-indel-limit N Exclude reads with more than N separate gaps.
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
845 default: ~unbounded
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
846 --standard-filters Use stringent input base and mapping quality filters
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
847 Equivalent to -m 30 -q 20 -R 0 -S 0
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
848 --min-alternate-fraction N Require at least this fraction of observations supporting
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
849 an alternate allele within a single individual in the
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
850 in order to evaluate the position. default: 0.05
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
851 --min-alternate-count N Require at least this count of observations supporting
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
852 an alternate allele within a single individual in order
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
853 to evaluate the position. default: 2
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
854 --min-alternate-qsum N Require at least this sum of quality of observations supporting
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
855 an alternate allele within a single individual in order
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
856 to evaluate the position. default: 0
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
857 --min-alternate-total N Require at least this count of observations supporting
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
858 an alternate allele within the total population in order
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
859 to use the allele in analysis. default: 1
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
860 --min-coverage N Require at least this coverage to process a site. default: 0
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
861 --limit-coverage N Downsample per-sample coverage to this level if greater than this coverage.
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
862 default: no limit
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
863 --skip-coverage N Skip processing of alignments overlapping positions with coverage >N.
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
864 This filters sites above this coverage, but will also reduce data nearby.
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
865 default: no limit
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
866
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
867 **Population priors**::
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
868
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
869 --no-population-priors Equivalent to --pooled-discrete --hwe-priors-off and removal of
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
870 Ewens Sampling Formula component of priors.
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
871
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
872 **Mappability priors**::
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
873
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
874 --hwe-priors-off Disable estimation of the probability of the combination
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
875 arising under HWE given the allele frequency as estimated
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
876 by observation frequency.
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
877 --binomial-obs-priors-off Disable incorporation of prior expectations about observations.
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
878 Uses read placement probability, strand balance probability,
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
879 and read position (5'-3') probability.
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
880 --allele-balance-priors-off Disable use of aggregate probability of observation balance between alleles
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
881 as a component of the priors.
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
882
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
883 **Genotype likelihoods**::
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
884
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
885 --observation-bias FILE Read length-dependent allele observation biases from FILE.
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
886 The format is [length] [alignment efficiency relative to reference]
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
887 where the efficiency is 1 if there is no relative observation bias.
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
888 --base-quality-cap Q Limit estimated observation quality by capping base quality at Q.
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
889 --prob-contamination F An estimate of contamination to use for all samples. default: 10e-9
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
890 --legacy-gls Use legacy (polybayes equivalent) genotype likelihood calculations
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
891 --contamination-estimates FILE A file containing per-sample estimates of contamination, such as
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
892 those generated by VerifyBamID. The format should be:
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
893 sample p(read=R|genotype=AR) p(read=A|genotype=AA)
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
894 Sample '*' can be used to set default contamination estimates.
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
895
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
896 **Algorithmic features**::
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
897
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
898 --report-genotype-likelihood-max Report genotypes using the maximum-likelihood estimate provided
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
899 from genotype likelihoods.
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
900 --genotyping-max-iterations N Iterate no more than N times during genotyping step. default: 1000.
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
901 --genotyping-max-banddepth N Integrate no deeper than the Nth best genotype by likelihood when
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
902 genotyping. default: 6.
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
903 --posterior-integration-limits N,M Integrate all genotype combinations in our posterior space
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
904 which include no more than N samples with their Mth best
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
905 data likelihood. default: 1,3.
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
906 --exclude-unobserved-genotypes Skip sample genotypings for which the sample has no supporting reads.
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
907 --genotype-variant-threshold N Limit posterior integration to samples where the second-best
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
908 genotype likelihood is no more than log(N) from the highest
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
909 genotype likelihood for the sample. default: ~unbounded
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
910 --use-mapping-quality Use mapping quality of alleles when calculating data likelihoods.
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
911 --harmonic-indel-quality Use a weighted sum of base qualities around an indel, scaled by the
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
912 distance from the indel. By default use a minimum BQ in flanking sequence.
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
913 --read-dependence-factor N Incorporate non-independence of reads by scaling successive
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
914 observations by this factor during data likelihood
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
915 calculations. default: 0.9
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
916 --genotype-qualities Calculate the marginal probability of genotypes and report as GQ in
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
917 each sample field in the VCF output.
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
918
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
919 ------
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
920
25
bf27106652f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 24
diff changeset
921 **Acknowledgments**
13
2dd40b601766 Uploaded
devteam
parents:
diff changeset
922
2dd40b601766 Uploaded
devteam
parents:
diff changeset
923 The initial version of the wrapper was produced by Dan Blankenberg and upgraded by Anton Nekrutenko.
28
977a5301b66d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 27
diff changeset
924 TNG was developed by Bjoern Gruening.
30
ef2c525bd8cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 29
diff changeset
925 ]]>
23
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 22
diff changeset
926 </help>
29
156b60c1530f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 99e8a87a2993ae644df15756044a40a42aa7a05b
iuc
parents: 28
diff changeset
927 <expand macro="citations">
156b60c1530f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 99e8a87a2993ae644df15756044a40a42aa7a05b
iuc
parents: 28
diff changeset
928 <citation type="bibtex">
156b60c1530f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 99e8a87a2993ae644df15756044a40a42aa7a05b
iuc
parents: 28
diff changeset
929 @article{Tange2011a,
156b60c1530f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 99e8a87a2993ae644df15756044a40a42aa7a05b
iuc
parents: 28
diff changeset
930 title = {GNU Parallel - The Command-Line Power Tool},
156b60c1530f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 99e8a87a2993ae644df15756044a40a42aa7a05b
iuc
parents: 28
diff changeset
931 author = {O. Tange},
156b60c1530f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 99e8a87a2993ae644df15756044a40a42aa7a05b
iuc
parents: 28
diff changeset
932 address = {Frederiksberg, Denmark},
156b60c1530f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 99e8a87a2993ae644df15756044a40a42aa7a05b
iuc
parents: 28
diff changeset
933 journal = {;login: The USENIX Magazine},
156b60c1530f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 99e8a87a2993ae644df15756044a40a42aa7a05b
iuc
parents: 28
diff changeset
934 month = {Feb},
156b60c1530f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 99e8a87a2993ae644df15756044a40a42aa7a05b
iuc
parents: 28
diff changeset
935 number = {1},
156b60c1530f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 99e8a87a2993ae644df15756044a40a42aa7a05b
iuc
parents: 28
diff changeset
936 volume = {36},
156b60c1530f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 99e8a87a2993ae644df15756044a40a42aa7a05b
iuc
parents: 28
diff changeset
937 url = {http://www.gnu.org/s/parallel},
156b60c1530f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 99e8a87a2993ae644df15756044a40a42aa7a05b
iuc
parents: 28
diff changeset
938 year = {2011},
156b60c1530f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 99e8a87a2993ae644df15756044a40a42aa7a05b
iuc
parents: 28
diff changeset
939 pages = {42-47}
156b60c1530f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 99e8a87a2993ae644df15756044a40a42aa7a05b
iuc
parents: 28
diff changeset
940 }
156b60c1530f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 99e8a87a2993ae644df15756044a40a42aa7a05b
iuc
parents: 28
diff changeset
941 </citation>
156b60c1530f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 99e8a87a2993ae644df15756044a40a42aa7a05b
iuc
parents: 28
diff changeset
942 </expand>
13
2dd40b601766 Uploaded
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parents:
diff changeset
943 </tool>