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annotate freebayes.xml @ 18:37da353c7689 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit fe6bd492e3188ec78ef4bc5111c5da40eae05b0a
author iuc
date Mon, 14 Oct 2024 09:01:47 +0000
parents a2feedafda6f
children 3ccfc2851e21
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a2feedafda6f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit be1c2e9e056710ef8b1110a121dc38c6e06dbbee"
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1 <tool id="freebayes" name="FreeBayes" version="@TOOL_VERSION@+galaxy0">
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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="5.3.1">gawk</requirement>
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11 <requirement type="package" version="20240922">parallel</requirement>
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12 </expand>
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13 <expand macro="version_command" />
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14 <command detect_errors="exit_code"><![CDATA[
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15 ##set up input files
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17 #set $reference_fasta_filename = "localref.fa"
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19 #if str( $reference_source.reference_source_selector ) == "history":
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20 ln -s -f '${reference_source.ref_file}' '${reference_fasta_filename}' &&
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21 samtools faidx '${reference_fasta_filename}' 2>&1 || echo "Error running samtools faidx for FreeBayes" >&2 &&
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22 #else:
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23 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
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24 #end if
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26 #if $reference_source.batchmode.processmode == 'merge':
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27 #set $input_bamfiles = $reference_source.batchmode.input_bams
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28 #else:
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29 #set $input_bamfiles = [ $reference_source.batchmode.input_bams ]
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30 #end if
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32 #for $bam_count, $input_bam in enumerate( $input_bamfiles ):
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33 #if $input_bam.ext == 'bam':
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34 ln -s -f '${input_bam}' 'b_${bam_count}.bam' &&
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35 ln -s -f '${input_bam.metadata.bam_index}' 'b_${bam_count}.bam.bai' &&
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36 #elif $input_bam.ext == 'cram':
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37 ln -s -f '${input_bam}' 'b_${bam_count}.cram' &&
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38 ln -s -f '${input_bam.metadata.cram_index}' 'b_${bam_count}.cram.crai' &&
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39 #end if
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40 #end for
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42 ## Tabixize optional input_variant_vcf file (for --variant-input option)
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43 #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( $options_type.optional_inputs.input_variant_type.input_variant_type_selector ) == "provide_vcf":
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44 ln -s -f '${options_type.optional_inputs.input_variant_type.input_variant_vcf}' input_variant_vcf.vcf.gz &&
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45 ln -s -f '${Tabixized_input}' input_variant_vcf.vcf.gz.tbi &&
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46 #end if
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47
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48 ##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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49 #if str( $target_limit_type.target_limit_type_selector ) == "limit_by_target_file":
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50 ln -s '${target_limit_type.input_target_bed}' regions_all.bed &&
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51 #elif str( $target_limit_type.target_limit_type_selector ) == "limit_by_region":
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52 printf '${target_limit_type.region_chromosome}\t${target_limit_type.region_start}\t${target_limit_type.region_end}' > regions_all.bed &&
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53 #else
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54 ##divide up the regions in the bam file for efficient processing
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55 #for $bam_count, $input_bam in enumerate( $input_bamfiles ):
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56 samtools view -H b_${bam_count}.${input_bam.ext}|
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57 grep '^@SQ' |
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58 cut -f 2- |
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59 awk '{ gsub("^SN:","",$1); gsub("^LN:","",$2); print $1"\t0\t"$2; }' >> regions_all.bed &&
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60 #end for
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61 #end if
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62
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63 sort -u regions_all.bed > regions_uniq.bed &&
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64 ## split into even small chunks, this has some disatvantages and will not be used for the moment
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65 ## bedtools makewindows -b regions_uniq.bed -w 10000000 -s 9990000 > regions.bed &&
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66
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67 mkdir vcf_output failed_alleles trace &&
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69 ## Finished setting up inputs
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71 for i in `cat regions_uniq.bed | awk '{print $1":"$2".."$3}'`;
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72 do
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73 echo "
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75 ## COMMAND LINE STARTS HERE
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77 freebayes
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79 --region '\$i'
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81 #for $bam_count, $input_bam in enumerate( $input_bamfiles ):
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82 --bam 'b_${bam_count}.${input_bam.ext}'
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83 #end for
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84 --fasta-reference '${reference_fasta_filename}'
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86 ## Outputs
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87 --vcf './vcf_output/part_\$i.vcf'
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88
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89 ## Coverage
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90 #if str($coverage_options.coverage_options_selector) == "set":
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91 @COVERAGE@
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92 #end if
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93
6
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94 ##advanced options
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95 #if str( $options_type.options_type_selector ) == "simple":
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96 #pass
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97 #elif str( $options_type.options_type_selector ) == "simple_w_filters":
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98 --standard-filters
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99 #elif str( $options_type.options_type_selector ) == "naive":
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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 #elif str( $options_type.options_type_selector ) == "naive_w_filters":
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106 --haplotype-length 0
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107 --min-alternate-count 1
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108 --min-alternate-fraction 0.05
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109 --pooled-continuous
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110 --report-monomorphic
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111 --standard-filters
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112 #elif str( $options_type.options_type_selector ) == "full":
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113 #if str( $options_type.optional_inputs.optional_inputs_selector ) == 'set':
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114 ${options_type.optional_inputs.report_monomorphic}
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115
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116 #if $options_type.optional_inputs.output_trace_option:
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117 --trace ./trace/part_'\$i'.txt
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118 #end if
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119 #if $options_type.optional_inputs.output_failed_alleles_option:
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120 --failed-alleles ./failed_alleles/part_'\$i'.bed
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121 #end if
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122 #if $options_type.optional_inputs.samples:
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123 --samples '${options_type.optional_inputs.samples}'
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124 #end if
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125 #if $options_type.optional_inputs.populations:
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126 --populations '${options_type.optional_inputs.populations}'
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127 #end if
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128 #if $options_type.optional_inputs.A:
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129 --cnv-map '${options_type.optional_inputs.A}'
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130 #end if
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131 #if str( $options_type.optional_inputs.input_variant_type.input_variant_type_selector ) == "provide_vcf":
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132 --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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133 ${options_type.optional_inputs.input_variant_type.only_use_input_alleles}
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134 #end if
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135 #if $options_type.optional_inputs.haplotype_basis_alleles:
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136 --haplotype-basis-alleles '${options_type.optional_inputs.haplotype_basis_alleles}'
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137 #end if
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138 #if $options_type.optional_inputs.observation_bias:
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139 --observation-bias '${options_type.optional_inputs.observation_bias}'
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140 #end if
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141 #if $options_type.optional_inputs.contamination_estimates:
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142 --contamination-estimates '${options_type.optional_inputs.contamination_estimates}'
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143 #end if
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144 $options_type.optional_inputs.trim_complex_tail
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145 #end if
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146
6
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147 ## REPORTING
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148 #if str( $options_type.reporting.reporting_selector ) == "set":
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149 --pvar ${options_type.reporting.pvar}
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150 #end if
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151 ## POPULATION MODEL
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152 #if str( $options_type.population_model.population_model_selector ) == "set":
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153 --theta ${options_type.population_model.T}
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154 --ploidy ${options_type.population_model.P}
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155 ${options_type.population_model.J}
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156 ${options_type.population_model.K}
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157 #end if
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158
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159 ## REFERENCE ALLELE
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160 #if str( $options_type.reference_allele.reference_allele_selector ) == "set":
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161 ${options_type.reference_allele.Z}
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162 --reference-quality '${options_type.reference_allele.reference_quality}'
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163 #end if
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164
6
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165 ## ALLELE SCOPE
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166 #if str( $options_type.allele_scope.allele_scope_selector ) == "set":
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167 ${options_type.allele_scope.I}
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168 ${options_type.allele_scope.i}
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169 ${options_type.allele_scope.X}
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170 ${options_type.allele_scope.u}
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171 ${options_type.allele_scope.no_partial_observations}
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172
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173 -n ${options_type.allele_scope.n}
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174
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175 --haplotype-length ${options_type.allele_scope.haplotype_length}
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176 --min-repeat-size ${options_type.allele_scope.min_repeat_length}
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177 --min-repeat-entropy ${options_type.allele_scope.min_repeat_entropy}
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178 #end if
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179
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180 ## REALIGNMENT
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181 ${options_type.O}
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182
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183 ##INPUT FILTERS
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184 #if str( $options_type.input_filters.input_filters_selector ) == "set":
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185 ${options_type.input_filters.standard_filters}
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186 ${options_type.input_filters.use_duplicate_reads}
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187 --min-mapping-quality ${options_type.input_filters.min_mapping_quality}
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188 --min-base-quality ${options_type.input_filters.min_base_quality}
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189 --min-supporting-allele-qsum ${options_type.input_filters.min_supporting_allele_qsum}
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190 --min-supporting-mapping-qsum ${options_type.input_filters.min_supporting_mapping_qsum}
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191 #if str( $options_type.input_filters.mismatch_filters.mismatch_filters_selector ) == "set":
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192 --mismatch-base-quality-threshold ${options_type.input_filters.mismatch_filters.mismatch_base_quality_threshold}
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193 #if str($options_type.input_filters.mismatch_filters.read_mismatch_limit)
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194 --read-mismatch-limit ${options_type.input_filters.mismatch_filters.read_mismatch_limit}
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195 #end if
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196 --read-max-mismatch-fraction ${options_type.input_filters.mismatch_filters.read_max_mismatch_fraction}
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197 --read-snp-limit ${options_type.input_filters.mismatch_filters.read_snp_limit}
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198 #end if
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199 --read-indel-limit ${options_type.input_filters.read_indel_limit}
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200 --min-alternate-fraction ${options_type.input_filters.min_alternate_fraction}
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201 --min-alternate-qsum ${options_type.input_filters.min_alternate_qsum}
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202 --min-alternate-count ${options_type.input_filters.min_alternate_count}
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203 --min-alternate-total ${options_type.input_filters.min_alternate_total}
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204 #end if
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205
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206 ## POPULATION AND MAPPABILITY PRIORS
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207 #if str( $options_type.population_mappability_priors.population_mappability_priors_selector ) == "set":
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208 ${options_type.population_mappability_priors.k}
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209 ${options_type.population_mappability_priors.w}
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210 ${options_type.population_mappability_priors.V}
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211 ${options_type.population_mappability_priors.a}
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212 #end if
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213
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214 ## GENOTYPE LIKELIHOODS
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215 #if str( $options_type.genotype_likelihoods.genotype_likelihoods_selector ) == "set":
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216 ${$options_type.genotype_likelihoods.experimental_gls}
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217
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218 --base-quality-cap ${$options_type.genotype_likelihoods.base_quality_cap}
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219 --prob-contamination ${$options_type.genotype_likelihoods.prob_contamination}
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220 #end if
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221
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222 ## ALGORITHMIC FEATURES
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223 #if str( $options_type.algorithmic_features.algorithmic_features_selector ) == "set":
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224 -B '${options_type.algorithmic_features.B}'
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225 -W '${options_type.algorithmic_features.W}'
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226 -D '${options_type.algorithmic_features.D}'
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227
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228 #if str($options_type.algorithmic_features.genotype_variant_threshold)
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229 -S ${options_type.algorithmic_features.genotype_variant_threshold}
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230 #end if
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231
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232 ${options_type.algorithmic_features.N}
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233 ${options_type.algorithmic_features.j}
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234 ${options_type.algorithmic_features.H}
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235 ${options_type.algorithmic_features.genotype_qualities}
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236 ${options_type.algorithmic_features.report_genotype_likelihood_max}
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237
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238 --genotyping-max-banddepth ${options_type.algorithmic_features.genotyping_max_banddepth}
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239 #end if
3
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240 #end if
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241
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242 ";
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243 done > freebayes_commands.sh &&
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244
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245 cat freebayes_commands.sh |
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246 parallel --will-cite -j \${GALAXY_SLOTS:-1} &&
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247
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248 ## make VCF header
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249 grep "^#" "./vcf_output/part_\$i.vcf" > header.txt &&
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250
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251 for i in `cat regions_uniq.bed | awk '{print $1":"$2".."$3}'`;
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252 do
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253 ## if this fails then it bails out the script
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254 cat "./vcf_output/part_\$i.vcf" | grep -v "^#" || true
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255 ;
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256 done | sort -k1,1 -k2,2n -k5,5 -u | cat header.txt - > '${output_vcf}'
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257
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258 #if str( $options_type.options_type_selector ) == "full":
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259 #if str( $options_type.optional_inputs.optional_inputs_selector ) == 'set':
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260 #if $options_type.optional_inputs.output_failed_alleles_option:
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261 &&
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262 for i in `cat regions.bed | awk '{print $1":"$2".."$3}'`;
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263 do
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264 cat "./failed_alleles/part_\$i.bed"
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265 ;
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266 done > '${output_failed_alleles_bed}'
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267 #end if
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268
4
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269 #if $options_type.optional_inputs.output_trace_option:
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270 &&
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271 for i in `cat regions.bed | awk '{print $1":"$2".."$3}'`;
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272 do
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273 cat './trace/part_\$i.txt'
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274 ;
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275 done > '${output_trace}'
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276 #end if
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277 #end if
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278 #end if
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279 ]]></command>
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280
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281 <inputs>
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282 <conditional name="reference_source">
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283 <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">
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284 <option value="cached">Locally cached</option>
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285 <option value="history">History</option>
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286 </param>
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287 <when value="cached">
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288 <expand macro="input_bam">
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289 <expand macro="validation" />
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290 </expand>
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291 <param name="ref_file" type="select" label="Using reference genome">
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292 <options from_data_table="fasta_indexes" />
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293 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input dataset"/>
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294 </param>
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295 </when>
4
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296 <when value="history"> <!-- FIX ME!!!! -->
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297 <expand macro="input_bam" />
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298 <param name="ref_file" type="data" format="fasta" label="Use the following dataset as the reference sequence"
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299 help="You can upload a FASTA sequence to the history and use it as reference" />
4
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300 </when>
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301 </conditional>
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302 <conditional name="target_limit_type">
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303 <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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304 <option value="do_not_limit" selected="true">Do not limit</option>
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305 <option value="limit_by_target_file">Limit by target file</option>
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306 <option value="limit_by_region">Limit to region</option>
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307 </param>
9
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308 <when value="do_not_limit" />
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309 <when value="limit_by_target_file">
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310 <param name="input_target_bed" argument="--targets" type="data" format="bed" label="Limit analysis to regions in this BED dataset" />
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311 </when>
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312 <when value="limit_by_region">
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313 <param name="region_chromosome" argument="--region" type="text" label="Region Chromosome" value="" /> <!--only once? -->
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314 <param name="region_start" type="integer" label="Region Start" value="" />
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315 <param name="region_end" type="integer" label="Region End" value="" />
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316 </when>
0
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317 </conditional>
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318 <conditional name="coverage_options">
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319 <param name="coverage_options_selector" type="select" label="Read coverage"
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320 help="Sets --min-coverage, --limit-coverage, and --skip-coverage">
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321 <option value="do_not_set" selected="true">Use defaults</option>
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322 <option value="set">Specify coverage options</option>
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323 </param>
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324 <when value="set">
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325 <expand macro="par_min_cov" />
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326 </when>
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327 <when value="do_not_set" />
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328 </conditional>
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329 <conditional name="options_type">
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330 <param name="options_type_selector" type="select" label="Choose parameter selection level"
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331 help="Select how much control over the freebayes run you need">
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332 <option value="simple" selected="true">1. Simple diploid calling</option>
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333 <option value="simple_w_filters">2. Simple diploid calling with filtering and coverage</option>
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334 <option value="naive">3. Frequency-based pooled calling</option>
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335 <option value="naive_w_filters">4. Frequency-based pooled calling with filtering and coverage</option>
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336 <option value="full">5. Full list of options</option>
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337 </param>
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338 <when value="full">
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339
4
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340 <conditional name="optional_inputs">
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341 <param name="optional_inputs_selector" type="select" label="Additional inputs"
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342 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, --contamination-estimates and --trim-complex-tail">
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343 <option value="do_not_set" selected="true">Do not provide additional inputs</option>
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344 <option value="set">Provide additional inputs</option>
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345 </param>
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346 <when value="set">
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347 <param name="output_failed_alleles_option" argument="--failed-alleles" type="boolean" truevalue="--failed-alleles" falsevalue="" checked="false"
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348 label="Write out failed alleles file" />
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349 <param name="output_trace_option" argument="--trace" type="boolean" truevalue="--trace" falsevalue="" checked="false"
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350 label="Write out algorithm trace file" />
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351 <param argument="--samples" type="data" format="txt"
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352 label="Limit analysis to samples listed (one per line) in this dataset" optional="true"
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353 help="By default FreeBayes will analyze all samples in its input BAM datasets" />
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354 <param argument="--populations" type="data" format="txt" optional="true"
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355 label="Populations dataset"
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356 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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357 <param name="A" argument="--cnv-map" type="data" format="bed" optional="true"
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358 label="Read a copy number map from a BED dataset"
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359 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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360 <conditional name="input_variant_type">
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361 <param name="input_variant_type_selector" type="select" label="Provide variants dataset">
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362 <option value="do_not_provide" selected="true">Do not provide</option>
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363 <option value="provide_vcf">Provide VCF dataset</option>
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364 </param>
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365 <when value="do_not_provide" />
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366 <when value="provide_vcf">
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367 <param name="input_variant_vcf" argument="--variant-input" type="data" format="vcf_bgzip"
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368 label="Use variants reported in this VCF dataset as input to the algorithm">
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369 <conversion name="Tabixized_input" type="tabix" />
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370 </param>
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371 <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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372 label="Only provide variant calls and genotype likelihoods for sites in VCF" />
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373 </when>
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374 </conditional>
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375 <param name="haplotype_basis_alleles" argument="--haplotype-basis-alleles" type="data" format="vcf" optional="true"
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376 label="Only use variant alleles provided in this input VCF for the construction of complex or haplotype alleles" />
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377 <param name="report_monomorphic" argument="--report-monomorphic" type="boolean" truevalue="--report-monomorphic" falsevalue="" checked="false"
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378 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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379 <param name="observation_bias" argument="--observation-bias" type="data" format="tabular" optional="true"
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380 label="Load read length-dependent allele observation biases from"
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381 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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382 <param name="contamination_estimates" argument="--contamination-estimates" type="data" format="tabular" optional="true"
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383 label="Upload per-sample estimates of contamination from"
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384 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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385 <param name="trim_complex_tail" argument="--trim-complex-tail" type="boolean" truevalue="--trim-complex-tail" falsevalue=""
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386 label="Trim trailing reference matches" />
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387 </when>
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388 <when value="do_not_set" />
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389 </conditional>
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390
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391 <!-- reporting -->
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392 <conditional name="reporting">
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393 <param name="reporting_selector" type="select" label="Reporting options" help="Sets -P --pvar option">
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394 <option value="do_not_set" selected="true">Use defaults</option>
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395 <option value="set">Set reporting options</option>
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diff changeset
396 </param>
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397 <when value="set">
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398 <param argument="--pvar" type="float" value="0.0"
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399 label="Report sites if the probability that there is a polymorphism at the site is greater than"
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400 help="Note that post-filtering is generally recommended over the use of this parameter" />
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401 </when>
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402 <when value="do_not_set" />
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403 </conditional>
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404
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405 <!-- population model -->
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406 <conditional name="population_model">
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407 <param name="population_model_selector" type="select" label="Population model options"
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408 help="Sets --theta, --ploidy, --pooled-discrete, and --pooled-continuous options">
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409 <option value="do_not_set" selected="true">Use defaults</option>
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410 <option value="set">Set population model options</option>
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411 </param>
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412 <when value="set">
9
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413 <param name="T" argument="--theta" type="float" value="0.001"
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414 label="The expected mutation rate or pairwise nucleotide diversity among the population under analysis"
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415 help="This serves as the single parameter to the Ewens Sampling Formula prior model" />
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416 <param name="P" argument="--ploidy" type="integer" value="2"
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417 label="Set ploidy for the analysis" />
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418 <param name="J" argument="--pooled-discrete" type="boolean" truevalue="-J" falsevalue="" checked="false"
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419 label="Assume that samples result from pooled sequencing"
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420 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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421 <param name="K" argument="--poled-continuous" type="boolean" truevalue="-K" falsevalue="" checked="false"
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422 label="Output all alleles which pass input filters, regardles of genotyping outcome or model" />
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423 </when>
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424 <when value="do_not_set" />
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425 </conditional>
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426
4
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diff changeset
427 <!-- reference allele -->
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428 <conditional name="reference_allele">
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429 <param name="reference_allele_selector" type="select" label="Reference allele options"
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430 help="Sets --use-reference-allele and --reference-quality options">
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431 <option value="do_not_set" selected="true">Use defaults</option>
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432 <option value="set">Set reference allele options</option>
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diff changeset
433 </param>
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434 <when value="set">
9
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435 <param name="Z" argument="--use-reference-allele" type="boolean" truevalue="-Z" falsevalue="" checked="false"
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diff changeset
436 label="Include the reference allele in the analysis as if it is another sample from the same population" />
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437 <param name="reference_quality" argument="--reference-quality" type="text" value="100,60"
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diff changeset
438 label="Assign mapping quality of MQ (100) to the reference allele at each site and base quality of BQ (60)" />
4
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439 </when>
9
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parents: 8
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440 <when value="do_not_set" />
4
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441 </conditional>
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442
4
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diff changeset
443 <!-- allelic scope -->
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444 <conditional name="allele_scope">
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445 <param name="allele_scope_selector" type="select" label="Allelic scope options"
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446 help="Sets -I, i, -X, -u, -n, --haplotype-length, --min-repeat-size, --min-repeat-entropy, and --no-partial-observations options">
4
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447 <option value="do_not_set" selected="true">Use defaults</option>
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448 <option value="set">Set alleic scope options</option>
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diff changeset
449 </param>
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450 <when value="set">
9
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451 <param name="I" argument="--no-snps" type="boolean" truevalue="-I" falsevalue="" checked="false"
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452 label="Ignore SNP alleles" />
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parents: 8
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453 <param name="i" argument="--no-indels" type="boolean" truevalue="-i" falsevalue="" checked="false"
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parents: 8
diff changeset
454 label="Ignore indels alleles" />
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parents: 8
diff changeset
455 <param name="X" argument="--no-mnps" type="boolean" truevalue="-X" falsevalue="" checked="false"
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parents: 8
diff changeset
456 label="Ignore multi-nucleotide polymorphisms, MNPs" />
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parents: 8
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457 <param name="u" argument="--no-complex" type="boolean" truevalue="-u" falsevalue="" checked="false"
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parents: 8
diff changeset
458 label="Ignore complex events (composites of other classes)" />
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parents: 8
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459 <param name="n" argument="--use-best-n-alleles" type="integer" value="0"
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parents: 8
diff changeset
460 label="How many best SNP alleles to evaluate"
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461 help="Alleles are ranked by the sum of supporting quality scores. Set to 0 to evaluate all" />
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462 <param name="haplotype_length" argument="--haplotype-length" type="integer" value="3"
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diff changeset
463 label="Allow haplotype calls with contiguous embedded matches of up to (nucleotides)" />
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parents: 8
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464 <param name="min_repeat_length" argument="--min-repeat-size" type="integer" value="5"
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diff changeset
465 label="When assembling observations across repeats, require the total repeat length at least this many bp" />
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parents: 10
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466 <param name="min_repeat_entropy" argument="--min-repeat-entropy" type="integer" value="1"
9
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parents: 8
diff changeset
467 label="To detect interrupted repeats, build across sequence until it has entropy > (bits per bp)" />
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468 <param name="no_partial_observations" argument="--no-partial-observations" type="boolean" truevalue="--no-partial-observations" falsevalue="" checked="false"
6
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parents: 5
diff changeset
469 label="Exclude observations which do not fully span the dynamically-determined detection window"
9
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diff changeset
470 help="By default, FreeBayes uses all observations, dividing partial support across matching haplotypes when generating haplotypes" />
4
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diff changeset
471 </when>
9
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parents: 8
diff changeset
472 <when value="do_not_set" />
4
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diff changeset
473 </conditional>
6
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parents: 5
diff changeset
474
4
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diff changeset
475 <!-- indel realignment -->
9
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parents: 8
diff changeset
476 <param name="O" argument="--dont-left-align-indels" type="boolean" truevalue="-O" falsevalue="" checked="false"
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diff changeset
477 label="Turn off left-alignment of indels" />
6
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parents: 5
diff changeset
478
4
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parents: 3
diff changeset
479 <!-- input filters -->
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diff changeset
480 <conditional name="input_filters">
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diff changeset
481 <param name="input_filters_selector" type="select" label="Input filters">
4
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diff changeset
482 <option value="do_not_set" selected="true">No input filters (default)</option>
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diff changeset
483 <option value="set">Set input filters</option>
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diff changeset
484 </param>
6
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parents: 5
diff changeset
485 <when value="set">
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diff changeset
486 <param argument="--standard-filters" type="boolean" truevalue="--standard-filters" falsevalue="" checked="false"
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diff changeset
487 label="Use stringent input base and mapping quality filters"
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parents: 12
diff changeset
488 help="--min-mapping-quality 30 --min-base-quality 20, --min-supporting-allele-qsum 0 --genotype-variant-threshold 0"/>
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parents: 12
diff changeset
489 <param argument="--use-duplicate-reads" type="boolean" truevalue="--use-duplicate-reads" falsevalue="" checked="false"
9
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diff changeset
490 label="Include duplicate-marked alignments in the analysis" />
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parents: 12
diff changeset
491 <param argument="--min-mapping-quality" type="integer" value="1"
9
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diff changeset
492 label="Exclude alignments from analysis if they have a mapping quality less than" />
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parents: 12
diff changeset
493 <param argument="--min-base-quality" type="integer" value="0"
9
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diff changeset
494 label="Exclude alleles from analysis if their supporting base quality less than" />
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parents: 12
diff changeset
495 <param argument="--min-supporting-allele-qsum" type="integer" value="0"
9
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diff changeset
496 label="Consider any allele in which the sum of qualities of supporting observations is at least" />
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parents: 12
diff changeset
497 <param argument="--min-supporting-mapping-qsum" type="integer" value="0"
9
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parents: 8
diff changeset
498 label="Consider any allele in which and the sum of mapping qualities of supporting reads is at least" />
4
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parents: 3
diff changeset
499 <conditional name="mismatch_filters">
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500 <param name="mismatch_filters_selector" type="select" label="Mismatch filters"
6
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parents: 5
diff changeset
501 help="Sets -Q, -U, -z, and &#36; options">
4
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parents: 3
diff changeset
502 <option value="do_not_set" selected="true">No mismatch filters (default)</option>
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parents: 3
diff changeset
503 <option value="set">Set mismatch filters</option>
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parents: 3
diff changeset
504 </param>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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parents: 3
diff changeset
505 <when value="set">
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parents: 12
diff changeset
506 <param argument="--mismatch-base-quality-threshold" type="integer" value="10"
9
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parents: 8
diff changeset
507 label="Count mismatches toward -U (option below) if the base quality of the mismatch is >=" />
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parents: 12
diff changeset
508 <param argument="--read-mismatch-limit" type="integer" value="1000" optional="true"
9
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parents: 8
diff changeset
509 label="Exclude reads with more than N mismatches where each mismatch has base quality >= mismatch-base-quality-threshold (option above)"
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parents: 8
diff changeset
510 help="default=~unbounded" />
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parents: 12
diff changeset
511 <param argument="--read-max-mismatch-fraction" type="float" value="1.0" min="0.0" max="1.0"
9
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parents: 8
diff changeset
512 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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diff changeset
513 <param name="read_snp_limit" argument="--read-snp-limit" type="integer" value="1000"
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parents: 8
diff changeset
514 label="Exclude reads with more than N base mismatches, ignoring gaps with quality >= mismatch-base-quality-threshold (third option above)"
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parents: 8
diff changeset
515 help="default=~unbounded" />
4
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parents: 3
diff changeset
516 </when>
9
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parents: 8
diff changeset
517 <when value="do_not_set" />
4
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parents: 3
diff changeset
518 </conditional>
13
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parents: 12
diff changeset
519 <param argument="--read-indel-limit" type="integer" value="1000"
9
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
520 label="Exclude reads with more than this number of separate gaps"
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
521 help="default=~unbounded" />
13
5031b6656a2b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 3b5abd63372c2806870627e9dc2a2f0f52f2e52a"
iuc
parents: 12
diff changeset
522 <param argument="--min-alternate-fraction" type="float" value="0.05"
9
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parents: 8
diff changeset
523 label="Require at least this fraction of observations supporting an alternate allele within a single individual in the in order to evaluate the position" />
13
5031b6656a2b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 3b5abd63372c2806870627e9dc2a2f0f52f2e52a"
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parents: 12
diff changeset
524 <param argument="--min-alternate-qsum" type="integer" value="0"
5031b6656a2b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 3b5abd63372c2806870627e9dc2a2f0f52f2e52a"
iuc
parents: 12
diff changeset
525 label="Require at least this sum of quality of observations supporting an alternate allele within a single individual in order to evaluate the position" />
5031b6656a2b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 3b5abd63372c2806870627e9dc2a2f0f52f2e52a"
iuc
parents: 12
diff changeset
526 <param argument="--min-alternate-count" type="integer" value="2"
9
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iuc
parents: 8
diff changeset
527 label="Require at least this count of observations supporting an alternate allele within a single individual in order to evaluate the position" />
13
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iuc
parents: 12
diff changeset
528 <param argument="--min-alternate-total" type="integer" value="1"
9
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parents: 8
diff changeset
529 label="Require at least this count of observations supporting an alternate allele within the total population in order to use the allele in analysis" />
4
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parents: 3
diff changeset
530 </when>
9
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iuc
parents: 8
diff changeset
531 <when value="do_not_set" />
4
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devteam
parents: 3
diff changeset
532 </conditional>
6
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parents: 5
diff changeset
533
4
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parents: 3
diff changeset
534 <!-- population and mappability priors -->
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parents: 3
diff changeset
535 <conditional name="population_mappability_priors">
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parents: 3
diff changeset
536 <param name="population_mappability_priors_selector" type="select" label="Population and mappability priors"
9
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parents: 8
diff changeset
537 help="Sets -k, -w, -V, and -a options">
4
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parents: 3
diff changeset
538 <option value="do_not_set" selected="true">Use defaults</option>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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parents: 3
diff changeset
539 <option value="set">Set population and mappability priors</option>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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parents: 3
diff changeset
540 </param>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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parents: 3
diff changeset
541 <when value="set">
9
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iuc
parents: 8
diff changeset
542 <param name="k" argument="--no-population-priors" type="boolean" truevalue="-k" falsevalue="" checked="false"
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
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parents: 8
diff changeset
543 label="No population priors"
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
544 help="Equivalent to --pooled-discrete --hwe-priors-off and removal of Ewens Sampling Formula component of priors" />
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
545 <param name="w" argument="--hwe-priors-off" type="boolean" truevalue="-w" falsevalue="" checked="false"
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
546 label="Disable estimation of the probability of the combination arising under HWE given the allele frequency as estimated by observation frequency" />
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
547 <param name="V" argument="--binomial-obs-priors-off" type="boolean" truevalue="-V" falsevalue="" checked="false"
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
548 label="Disable incorporation of prior expectations about observations"
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
549 help="Uses read placement probability, strand balance probability, and read position (5&#39;'-3&#39;') probability" />
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
550 <param name="a" argument="--allele-balance-priors-off" type="boolean" truevalue="-a" falsevalue="" checked="false"
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
551 label="Disable use of aggregate probability of observation balance between alleles as a component of the priors" />
4
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parents: 3
diff changeset
552 </when>
9
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
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parents: 8
diff changeset
553 <when value="do_not_set" />
4
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parents: 3
diff changeset
554 </conditional>
6
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iuc
parents: 5
diff changeset
555
4
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parents: 3
diff changeset
556 <!-- genotype likelihoods -->
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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parents: 3
diff changeset
557 <conditional name="genotype_likelihoods">
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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parents: 3
diff changeset
558 <param name="genotype_likelihoods_selector" type="select" label="Genotype likelihood options"
9
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
559 help="Sets --base-quality-cap, --experimental-gls, and --prob-contamination options">
4
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parents: 3
diff changeset
560 <option value="do_not_set" selected="true">Use defaults</option>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
561 <option value="set">Set genotype likelihood options</option>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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parents: 3
diff changeset
562 </param>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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parents: 3
diff changeset
563 <when value="set">
9
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
564 <param name="base_quality_cap" argument="--base-quality-cap" type="integer" value="0"
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
565 label="Limit estimated observation quality by capping base quality at" />
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
566 <param name="experimental_gls" argument="--experimental-gls" type="boolean" truevalue="--experimental-gls" falsevalue="" checked="false"
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
567 label="Generate genotype likelihoods using 'effective base depth' metric qual = 1-BaseQual * 1-MapQual"
9
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
568 help="Incorporate partial observations. This is the default when contamination estimates are provided. Optimized for diploid samples" />
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
569 <param name="prob_contamination" argument="--prob-contamination" type="float" value="10e-9"
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
570 label="An estimate of contamination to use for all samples" />
4
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parents: 3
diff changeset
571 </when>
9
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iuc
parents: 8
diff changeset
572 <when value="do_not_set" />
4
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devteam
parents: 3
diff changeset
573 </conditional>
6
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parents: 5
diff changeset
574
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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parents: 3
diff changeset
575 <!-- algorithmic features -->
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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parents: 3
diff changeset
576 <conditional name="algorithmic_features">
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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parents: 3
diff changeset
577 <param name="algorithmic_features_selector" type="select" label="Algorithmic features"
6
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parents: 5
diff changeset
578 help="Sets --report-genotypes-likelihood-max, -B, --genotyping-max-banddepth, -W, -N, S, -j, -H, -D, -= options">
4
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parents: 3
diff changeset
579 <option value="do_not_set" selected="true">Use defaults</option>
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parents: 3
diff changeset
580 <option value="set">Set algorithmic features</option>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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parents: 3
diff changeset
581 </param>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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parents: 3
diff changeset
582 <when value="set">
9
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
583 <param name="report_genotype_likelihood_max" argument="--report-genotype-likelihood-max" type="boolean" truevalue="--report-genotype-likelihood-max" falsevalue="" checked="false"
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
584 label="Report genotypes using the maximum-likelihood estimate provided from genotype likelihoods" />
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
585 <param name="B" argument="--genotyping-max-iterations" type="integer" value="1000"
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
586 label="Iterate no more than N times during genotyping step" />
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
587 <param name="genotyping_max_banddepth" argument="--genotyping-max-banddepth" type="integer" value="6"
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
588 label="Integrate no deeper than the Nth best genotype by likelihood when genotyping" />
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
589 <param name="W" argument="--posterior-integration-limits" type="text" value="1,3"
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
590 label="Integrate all genotype combinations in our posterior space which include no more than N (1) samples with their Mth (3) best data likelihood" />
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
591 <param name="N" argument="--exclude-unobserved-genotypes" type="boolean" truevalue="--exclude-unobserved-genotypes" falsevalue="" checked="false"
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
592 label="Skip sample genotypings for which the sample has no supporting reads" />
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
593 <param name="genotype_variant_threshold" argument="--genotype-variant-threshold" type="integer" value="" optional="true"
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
594 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"
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
595 help="default=~unbounded" />
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
596 <param name="j" argument="--use-mapping-quality" type="boolean" truevalue="-j" falsevalue="" checked="false"
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
597 label="Use mapping quality of alleles when calculating data likelihoods" />
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
598 <param name="H" argument="--harmonic-indel-quality" type="boolean" truevalue="-H" falsevalue="" checked="false"
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
599 label="Use a weighted sum of base qualities around an indel, scaled by the distance from the indel"
9
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
600 help="By default, FreeBayes uses a minimum Base Quality in flanking sequence" />
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
601 <param name="D" argument="--read-dependence-factor" type="float" value="0.9"
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
602 label="Incorporate non-independence of reads by scaling successive observations by this factor during data likelihood calculations" />
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
603 <param name="genotype_qualities" argument="--genotype-qualities" type="boolean" truevalue="--genotype-qualities" falsevalue="" checked="false"
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
604 label="Calculate the marginal probability of genotypes and report as GQ in each sample field in the VCF output" />
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
605 </when>
9
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
606 <when value="do_not_set" />
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
607 </conditional>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
608 </when>
9
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
609 <when value="simple" />
11
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iuc
parents: 10
diff changeset
610 <when value="simple_w_filters" />
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
611 <when value="naive" />
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
612 <when value="naive_w_filters" />
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
613 </conditional>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
614 </inputs>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
615 <outputs>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
616 <data format="vcf" name="output_vcf" label="${tool.name} on ${on_string} (variants)" />
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
617 <data format="bed" name="output_failed_alleles_bed" label="${tool.name} on ${on_string} (failed alleles)">
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
618 <filter>( options_type['options_type_selector'] == 'cline' or options_type['options_type_selector'] == 'full' ) and options_type['optional_inputs']['optional_inputs_selector'] == 'set' and options_type['optional_inputs']['output_failed_alleles_option'] is True</filter>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
619 </data>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
620 <data format="txt" name="output_trace" label="${tool.name} on ${on_string} (trace)">
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
621 <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>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
622 </data>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
623 </outputs>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
624 <tests>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
625 <test>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
626 <param name="reference_source_selector" value="history" />
8
b0ff6447545f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit d2f9b1728a6525b599e2c014a183b0415b27a870
iuc
parents: 7
diff changeset
627 <param name="processmode" value="individual" />
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
628 <param name="ref_file" ftype="fasta" value="freebayes-phix174.fasta"/>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
629 <param name="input_bams" ftype="bam" value="freebayes-phix174.bam"/>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
630 <param name="options_type_selector" value="simple"/>
10
2fb16f415220 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 99e8a87a2993ae644df15756044a40a42aa7a05b
iuc
parents: 9
diff changeset
631 <output name="output_vcf" file="freebayes-phix174-test1.vcf" lines_diff="4" />
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
632 </test>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
633 <test>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
634 <param name="reference_source_selector" value="history" />
8
b0ff6447545f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit d2f9b1728a6525b599e2c014a183b0415b27a870
iuc
parents: 7
diff changeset
635 <param name="processmode" value="individual" />
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
636 <param name="ref_file" ftype="fasta" value="freebayes-phix174.fasta"/>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
637 <param name="input_bams" ftype="bam" value="freebayes-phix174.bam"/>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
638 <param name="options_type_selector" value="naive_w_filters"/>
11
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
639 <param name="coverage_options_selector" value="set" />
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
640 <param name="min_coverage" value="14"/>
10
2fb16f415220 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 99e8a87a2993ae644df15756044a40a42aa7a05b
iuc
parents: 9
diff changeset
641 <output name="output_vcf" file="freebayes-phix174-test2.vcf" lines_diff="4" />
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
642 </test>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
643 <test>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
644 <param name="reference_source_selector" value="history" />
8
b0ff6447545f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit d2f9b1728a6525b599e2c014a183b0415b27a870
iuc
parents: 7
diff changeset
645 <param name="processmode" value="individual" />
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
646 <param name="ref_file" ftype="fasta" value="freebayes-phix174.fasta"/>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
647 <param name="input_bams" ftype="bam" value="freebayes-phix174.bam"/>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
648 <param name="options_type_selector" value="naive_w_filters"/>
11
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
649 <param name="coverage_options_selector" value="set" />
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
650 <param name="min_coverage" value="14"/>
10
2fb16f415220 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 99e8a87a2993ae644df15756044a40a42aa7a05b
iuc
parents: 9
diff changeset
651 <output name="output_vcf" file="freebayes-phix174-test3.vcf" lines_diff="4" />
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
652 </test>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
653 <test>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
654 <param name="reference_source_selector" value="history" />
8
b0ff6447545f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit d2f9b1728a6525b599e2c014a183b0415b27a870
iuc
parents: 7
diff changeset
655 <param name="processmode" value="individual" />
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
656 <param name="ref_file" ftype="fasta" value="freebayes-phix174.fasta"/>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
657 <param name="input_bams" ftype="bam" value="freebayes-phix174.bam"/>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
658 <param name="options_type_selector" value="full"/>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
659 <param name="population_model_selector" value="set"/>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
660 <param name="P" value="1"/>
14
91271de440f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit cce7fcdd5e8ba8636c751f9f974bf07a6845ba1c"
iuc
parents: 13
diff changeset
661 <param name="trim_complex_tail" value="--trim-complex-tail"/>
10
2fb16f415220 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 99e8a87a2993ae644df15756044a40a42aa7a05b
iuc
parents: 9
diff changeset
662 <output name="output_vcf" file="freebayes-phix174-test4.vcf" lines_diff="4" />
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
663 </test>
11
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
664 <test>
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
665 <param name="reference_source_selector" value="history" />
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
666 <param name="processmode" value="individual" />
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
667 <param name="ref_file" ftype="fasta" value="freebayes-hxb2.fasta"/>
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
668 <param name="input_bams" ftype="bam" value="freebayes-hxb2.bam"/>
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
669 <param name="options_type_selector" value="simple"/>
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
670 <param name="coverage_options_selector" value="set" />
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
671 <param name="min_coverage" value="250" />
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
672 <output name="output_vcf" file="freebayes-hxb2-test5.vcf" lines_diff="4" />
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
673 </test>
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
674 <test>
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
675 <param name="reference_source_selector" value="history" />
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
676 <param name="processmode" value="individual" />
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
677 <param name="ref_file" ftype="fasta" value="freebayes-hxb2.fasta"/>
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
678 <param name="input_bams" ftype="bam" value="freebayes-hxb2.bam"/>
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
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679 <param name="options_type_selector" value="simple"/>
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
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680 <param name="coverage_options_selector" value="set" />
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
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681 <param name="limit_coverage" value="400" />
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
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682 <output name="output_vcf" file="freebayes-hxb2-test6.vcf" lines_diff="4" />
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
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683 </test>
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
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684 <test>
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
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685 <param name="reference_source_selector" value="history" />
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
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686 <param name="processmode" value="individual" />
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
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687 <param name="ref_file" ftype="fasta" value="freebayes-hxb2.fasta"/>
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
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688 <param name="input_bams" ftype="bam" value="freebayes-hxb2.bam"/>
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
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689 <param name="options_type_selector" value="simple"/>
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
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690 <param name="coverage_options_selector" value="set" />
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
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691 <param name="skip_coverage" value="100" />
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
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692 <output name="output_vcf" file="freebayes-hxb2-test7.vcf" lines_diff="4" />
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
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693 </test>
14
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694 <test> <!-- Test with CRAM -->
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695 <param name="reference_source_selector" value="history" />
91271de440f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit cce7fcdd5e8ba8636c751f9f974bf07a6845ba1c"
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696 <param name="processmode" value="individual" />
91271de440f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit cce7fcdd5e8ba8636c751f9f974bf07a6845ba1c"
iuc
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697 <param name="ref_file" ftype="fasta" value="freebayes-phix174.fasta"/>
91271de440f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit cce7fcdd5e8ba8636c751f9f974bf07a6845ba1c"
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diff changeset
698 <param name="input_bams" ftype="cram" value="freebayes-phix174.cram"/>
91271de440f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit cce7fcdd5e8ba8636c751f9f974bf07a6845ba1c"
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699 <param name="options_type_selector" value="simple"/>
16
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700 <output name="output_vcf" file="freebayes-phix174-test1.vcf" lines_diff="6" />
14
91271de440f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit cce7fcdd5e8ba8636c751f9f974bf07a6845ba1c"
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701 </test>
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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702 </tests>
11
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
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diff changeset
703 <help><![CDATA[
0
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diff changeset
704 **What it does**
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705
2
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706 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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707
2
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708 See https://github.com/ekg/freebayes for details on FreeBayes.
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709
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710 ------
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711
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712 **Description**
0
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713
9
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
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714 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.
2
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715
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716 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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717
2
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718 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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719
2
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720 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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721
2
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722 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.
0
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723
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724 -------
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725
2
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726 **Galaxy-specific options**
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727
9
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
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728 Galaxy allows five levels of control over FreeBayes options, provided by the **Choose parameter selection level** menu option. These are:
0
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729
9
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
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730 1. *Simple diploid calling*: The simplest possible FreeBayes application. Equivalent to using FreeBayes with only a BAM input and no other parameter options.
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
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731 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.
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
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732 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.
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
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733 4. *Frequency-based pooled calling with filtering and coverage*: Same as #3 but adds -0 and --min-coverage like in #2.
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
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diff changeset
734 5. *Complete list of all options*: Gives you full control by exposing all FreeBayes options as Galaxy parameters.
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735
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736 ------
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737
11
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
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parents: 10
diff changeset
738 **Command-line parameters**
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
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diff changeset
739
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
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parents: 10
diff changeset
740 **Input**::
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
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diff changeset
741
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
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742 --bam FILE The file or set of BAM files to be analyzed.
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
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743 --bam-list FILE A file containing a list of BAM files to be analyzed.
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
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diff changeset
744
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
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745 --stdin Read BAM input on stdin.
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
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diff changeset
746 --fasta-reference FILE Use FILE as the reference sequence for analysis.
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
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747 An index file (FILE.fai) will be created if none exists.
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
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diff changeset
748 If neither --targets nor --region are specified, FreeBayes
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
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diff changeset
749 will analyze every position in this reference.
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
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750 --targets FILE Limit analysis to targets listed in the BED-format FILE.
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
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751 --region <chrom>:<start>-<end> Limit analysis to the specified region, 0-base coordinates,
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
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752 end_position not included (same as BED format).
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
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753 Either '-' or '..' maybe used as a separator.
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
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754 --samples FILE Limit analysis to samples listed (one per line) in the FILE.
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
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755 By default FreeBayes will analyze all samples in its input
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
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756 BAM files.
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
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757 --populations FILE Each line of FILE should list a sample and a population which
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
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758 it is part of. The population-based bayesian inference model
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
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759 will then be partitioned on the basis of the populations.
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
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760 --cnv-map FILE Read a copy number map from the BED file FILE, which has
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
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diff changeset
761 either a sample-level ploidy:
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
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762 sample_name copy_number
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
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763 or a region-specific format:
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
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diff changeset
764 seq_name start end sample_name copy_number
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
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765 ... for each region in each sample which does not have the
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
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766 default copy number as set by --ploidy. These fields can be delimited
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
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diff changeset
767 by space or tab.
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
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768
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
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769 **Output**::
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
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770
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
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771 --vcf FILE Output VCF-format results to FILE. (default: stdout)
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
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772 --gvcf Write gVCF output, which indicates coverage in uncalled regions.
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
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parents: 10
diff changeset
773 --gvcf-chunk NUM When writing gVCF output emit a record for every NUM bases.
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
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parents: 10
diff changeset
774 --gvcf-dont-use-chunk When writing the gVCF output emit a record for all bases if
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
775 set to "true" , will also route an int to --gvcf-chunk
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
776 similar to --output-mode EMIT_ALL_SITES from GATK
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
777 --variant-input VCF Use variants reported in VCF file as input to the algorithm.
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
778 Variants in this file will included in the output even if
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
779 there is not enough support in the data to pass input filters.
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
780 --only-use-input-alleles Only provide variant calls and genotype likelihoods for sites
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
781 and alleles which are provided in the VCF input, and provide
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
782 output in the VCF for all input alleles, not just those which
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
783 have support in the data.
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
784 --haplotype-basis-alleles VCF When specified, only variant alleles provided in this input
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
785 VCF will be used for the construction of complex or haplotype
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
786 alleles.
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
787 --report-all-haplotype-alleles At sites where genotypes are made over haplotype alleles,
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
788 provide information about all alleles in output, not only
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
789 those which are called.
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
790 --report-monomorphic Report even loci which appear to be monomorphic, and report all
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
791 considered alleles, even those which are not in called genotypes.
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
792 Loci which do not have any potential alternates have '.' for ALT.
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
793 --pvar N Report sites if the probability that there is a polymorphism
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
794 at the site is greater than N. default: 0.0. Note that post-
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
795 filtering is generally recommended over the use of this parameter.
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
796 --strict-vcf Generate strict VCF format (FORMAT/GQ will be an int)
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
797
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
798 **Population model**::
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
799
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
800 --theta N The expected mutation rate or pairwise nucleotide diversity
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
801 among the population under analysis. This serves as the
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
802 single parameter to the Ewens Sampling Formula prior model
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
803 default: 0.001
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
804 --ploidy N Sets the default ploidy for the analysis to N. default: 2
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
805 --pooled-discrete Assume that samples result from pooled sequencing.
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
806 Model pooled samples using discrete genotypes across pools.
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
807 When using this flag, set --ploidy to the number of
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
808 alleles in each sample or use the --cnv-map to define
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
809 per-sample ploidy.
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
810 --pooled-continuous Output all alleles which pass input filters, regardles of
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
811 genotyping outcome or model.
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
812
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
813 **Reference allele**::
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
814
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
815 --use-reference-allele This flag includes the reference allele in the analysis as
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
816 if it is another sample from the same population.
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
817 --reference-quality MQ,BQ Assign mapping quality of MQ to the reference allele at each
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
818 site and base quality of BQ. default: 100,60
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
819
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
820 **Allele scope**::
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
821
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
822 --use-best-n-alleles N Evaluate only the best N SNP alleles, ranked by sum of
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
823 supporting quality scores. (Set to 0 to use all; default: all)
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
824 --max-complex-gap
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
825 --haplotype-length N Allow haplotype calls with contiguous embedded matches of up
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
826 to this length. Set N=-1 to disable clumping. (default: 3)
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
827 --min-repeat-size When assembling observations across repeats, require the total repeat
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
828 length at least this many bp. (default: 5)
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
829 --min-repeat-entropy N To detect interrupted repeats, build across sequence until it has
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
830 entropy > N bits per bp. Set to 0 to turn off. (default: 1)
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
831 --no-partial-observations Exclude observations which do not fully span the dynamically-determined
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
832 detection window. (default, use all observations, dividing partial
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
833 support across matching haplotypes when generating haplotypes.)
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
834
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
835 **Indel realignment**::
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
836
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
837 --dont-left-align-indels Turn off left-alignment of indels, which is enabled by default.
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
838
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
839 **Input filters**::
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
840
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
841 --use-duplicate-reads Include duplicate-marked alignments in the analysis.
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
842 default: exclude duplicates marked as such in alignments
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
843 --min-mapping-quality Q Exclude alignments from analysis if they have a mapping
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
844 quality less than Q. default: 1
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
845 --min-base-quality Q Exclude alleles from analysis if their supporting base
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
846 quality is less than Q. default: 0
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
847 --min-supporting-allele-qsum Q Consider any allele in which the sum of qualities of supporting
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
848 observations is at least Q. default: 0
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
849 --min-supporting-mapping-qsum Q Consider any allele in which and the sum of mapping qualities of
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
850 supporting reads is at least Q. default: 0
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
851 --mismatch-base-quality-threshold Q Count mismatches toward --read-mismatch-limit if the base
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
852 quality of the mismatch is >= Q. default: 10
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
853 --read-mismatch-limit N Exclude reads with more than N mismatches where each mismatch
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
854 has base quality >= mismatch-base-quality-threshold.
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
855 default: ~unbounded
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
856 --read-max-mismatch-fraction N Exclude reads with more than N [0,1] fraction of mismatches where
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
857 each mismatch has base quality >= mismatch-base-quality-threshold
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
858 default: 1.0
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
859 --read-snp-limit N Exclude reads with more than N base mismatches, ignoring gaps
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
860 with quality >= mismatch-base-quality-threshold.
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
861 default: ~unbounded
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
862 --read-indel-limit N Exclude reads with more than N separate gaps.
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
863 default: ~unbounded
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
864 --standard-filters Use stringent input base and mapping quality filters
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
865 Equivalent to -m 30 -q 20 -R 0 -S 0
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
866 --min-alternate-fraction N Require at least this fraction of observations supporting
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
867 an alternate allele within a single individual in the
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
868 in order to evaluate the position. default: 0.05
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
869 --min-alternate-count N Require at least this count of observations supporting
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
870 an alternate allele within a single individual in order
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
871 to evaluate the position. default: 2
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
872 --min-alternate-qsum N Require at least this sum of quality of observations supporting
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
873 an alternate allele within a single individual in order
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
874 to evaluate the position. default: 0
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
875 --min-alternate-total N Require at least this count of observations supporting
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
876 an alternate allele within the total population in order
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
877 to use the allele in analysis. default: 1
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
878 --min-coverage N Require at least this coverage to process a site. default: 0
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
879 --limit-coverage N Downsample per-sample coverage to this level if greater than this coverage.
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
880 default: no limit
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
881 --skip-coverage N Skip processing of alignments overlapping positions with coverage >N.
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
882 This filters sites above this coverage, but will also reduce data nearby.
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
883 default: no limit
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
884
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
885 **Population priors**::
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
886
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
887 --no-population-priors Equivalent to --pooled-discrete --hwe-priors-off and removal of
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
888 Ewens Sampling Formula component of priors.
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
889
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
890 **Mappability priors**::
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
891
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
892 --hwe-priors-off Disable estimation of the probability of the combination
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
893 arising under HWE given the allele frequency as estimated
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
894 by observation frequency.
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
895 --binomial-obs-priors-off Disable incorporation of prior expectations about observations.
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
896 Uses read placement probability, strand balance probability,
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
897 and read position (5'-3') probability.
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
898 --allele-balance-priors-off Disable use of aggregate probability of observation balance between alleles
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
899 as a component of the priors.
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
900
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
901 **Genotype likelihoods**::
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
902
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
903 --observation-bias FILE Read length-dependent allele observation biases from FILE.
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
904 The format is [length] [alignment efficiency relative to reference]
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
905 where the efficiency is 1 if there is no relative observation bias.
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
906 --base-quality-cap Q Limit estimated observation quality by capping base quality at Q.
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
907 --prob-contamination F An estimate of contamination to use for all samples. default: 10e-9
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
908 --legacy-gls Use legacy (polybayes equivalent) genotype likelihood calculations
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
909 --contamination-estimates FILE A file containing per-sample estimates of contamination, such as
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
910 those generated by VerifyBamID. The format should be:
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
911 sample p(read=R|genotype=AR) p(read=A|genotype=AA)
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
912 Sample '*' can be used to set default contamination estimates.
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
913
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
914 **Algorithmic features**::
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
915
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
916 --report-genotype-likelihood-max Report genotypes using the maximum-likelihood estimate provided
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
917 from genotype likelihoods.
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
918 --genotyping-max-iterations N Iterate no more than N times during genotyping step. default: 1000.
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
919 --genotyping-max-banddepth N Integrate no deeper than the Nth best genotype by likelihood when
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
920 genotyping. default: 6.
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
921 --posterior-integration-limits N,M Integrate all genotype combinations in our posterior space
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
922 which include no more than N samples with their Mth best
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
923 data likelihood. default: 1,3.
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
924 --exclude-unobserved-genotypes Skip sample genotypings for which the sample has no supporting reads.
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
925 --genotype-variant-threshold N Limit posterior integration to samples where the second-best
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
926 genotype likelihood is no more than log(N) from the highest
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
927 genotype likelihood for the sample. default: ~unbounded
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
928 --use-mapping-quality Use mapping quality of alleles when calculating data likelihoods.
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
929 --harmonic-indel-quality Use a weighted sum of base qualities around an indel, scaled by the
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
930 distance from the indel. By default use a minimum BQ in flanking sequence.
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
931 --read-dependence-factor N Incorporate non-independence of reads by scaling successive
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
932 observations by this factor during data likelihood
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
933 calculations. default: 0.9
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
934 --genotype-qualities Calculate the marginal probability of genotypes and report as GQ in
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
935 each sample field in the VCF output.
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
936
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
937 ------
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
938
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
939 **Acknowledgments**
0
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
940
2
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
941 The initial version of the wrapper was produced by Dan Blankenberg and upgraded by Anton Nekrutenko.
9
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
942 TNG was developed by Bjoern Gruening.
11
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
943 ]]>
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
944 </help>
10
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945 <expand macro="citations">
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946 <citation type="bibtex">
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947 @article{Tange2011a,
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948 title = {GNU Parallel - The Command-Line Power Tool},
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949 author = {O. Tange},
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950 address = {Frederiksberg, Denmark},
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951 journal = {;login: The USENIX Magazine},
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952 month = {Feb},
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953 number = {1},
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954 volume = {36},
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955 url = {http://www.gnu.org/s/parallel},
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956 year = {2011},
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957 pages = {42-47}
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958 }
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959 </citation>
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960 </expand>
0
e21073b0dc1f Uploaded initial revision.
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961 </tool>