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annotate freebayes.xml @ 12:2667d6a97b50 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
author iuc
date Tue, 31 Aug 2021 08:10:08 +0000
parents f14331392369
children 5031b6656a2b
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f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
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1 <tool id="freebayes" name="FreeBayes" version="@DEPENDENCY_VERSION@">
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2 <description>bayesian genetic variant detector</description>
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3 <xrefs>
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4 <xref type="bio.tools">freebayes</xref>
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5 </xrefs>
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6 <macros>
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7 <import>macros.xml</import>
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8 </macros>
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9 <expand macro="requirements">
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10 <requirement type="package" version="4.1.3">gawk</requirement>
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11 <requirement type="package" version="20170422">parallel</requirement>
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12 </expand>
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
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13 <command detect_errors="exit_code"><![CDATA[
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14 ##set up input files
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15
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16 #set $reference_fasta_filename = "localref.fa"
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17
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18 #if str( $reference_source.reference_source_selector ) == "history":
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19 ln -s -f '${reference_source.ref_file}' '${reference_fasta_filename}' &&
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
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20 samtools faidx '${reference_fasta_filename}' 2>&1 || echo "Error running samtools faidx for FreeBayes" >&2 &&
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21 #else:
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22 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
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23 #end if
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25 #if $reference_source.batchmode.processmode == 'merge':
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26 #set $input_bamfiles = $reference_source.batchmode.input_bams
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27 #else:
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28 #set $input_bamfiles = [ $reference_source.batchmode.input_bams ]
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29 #end if
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31 #for $bam_count, $input_bam in enumerate( $input_bamfiles ):
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32 ln -s -f '${input_bam}' 'b_${bam_count}.bam' &&
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33 ln -s -f '${input_bam.metadata.bam_index}' 'b_${bam_count}.bam.bai' &&
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34 #end for
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35
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36 ## Tabixize optional input_variant_vcf file (for --variant-input option)
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37 #if ( str( $options_type.options_type_selector ) == 'cline' or str( $options_type.options_type_selector ) == 'full' ) and str( $options_type.optional_inputs.optional_inputs_selector ) == 'set' and str( $options_type.optional_inputs.input_variant_type.input_variant_type_selector ) == "provide_vcf":
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38 ln -s -f '${options_type.optional_inputs.input_variant_type.input_variant_vcf}' input_variant_vcf.vcf.gz &&
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39 ln -s -f '${Tabixized_input}' input_variant_vcf.vcf.gz.tbi &&
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40 #end if
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41
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42 ##if the user has specified a region or target file, just use that instead of calculating a set of unique regions
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43 #if str( $target_limit_type.target_limit_type_selector ) == "limit_by_target_file":
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44 ln -s '${target_limit_type.input_target_bed}' regions_all.bed &&
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45 #elif str( $target_limit_type.target_limit_type_selector ) == "limit_by_region":
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46 printf '${target_limit_type.region_chromosome}\t${target_limit_type.region_start}\t${target_limit_type.region_end}' > regions_all.bed &&
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47 #else
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48 ##divide up the regions in the bam file for efficient processing
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49 #for $bam_count, $input_bam in enumerate( $input_bamfiles ):
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50 samtools view -H b_${bam_count}.bam |
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51 grep '^@SQ' |
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52 cut -f 2- |
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53 awk '{ gsub("^SN:","",$1); gsub("^LN:","",$2); print $1"\t0\t"$2; }' >> regions_all.bed &&
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54 #end for
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55 #end if
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56
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57 sort -u regions_all.bed > regions_uniq.bed &&
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58 ## split into even small chunks, this has some disatvantages and will not be used for the moment
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59 ## bedtools makewindows -b regions_uniq.bed -w 10000000 -s 9990000 > regions.bed &&
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60
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61 mkdir vcf_output failed_alleles trace &&
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63 ## Finished setting up inputs
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64
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65 for i in `cat regions_uniq.bed | awk '{print $1":"$2".."$3}'`;
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66 do
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67 echo "
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68
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69 ## COMMAND LINE STARTS HERE
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70
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71 freebayes
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72
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73 --region '\$i'
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74
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75 #for $bam_count, $input_bam in enumerate( $input_bamfiles ):
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76 --bam 'b_${bam_count}.bam'
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77 #end for
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78 --fasta-reference '${reference_fasta_filename}'
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79
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80 ## Outputs
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81 --vcf './vcf_output/part_\$i.vcf'
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82
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83 ## Coverage
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84 #if str($coverage_options.coverage_options_selector) == "set":
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85 @COVERAGE@
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86 #end if
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87
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88 ##advanced options
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89 #if str( $options_type.options_type_selector ) == "simple":
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90 #pass
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91 #elif str( $options_type.options_type_selector ) == "simple_w_filters":
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92 --standard-filters
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93 #elif str( $options_type.options_type_selector ) == "naive":
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94 --haplotype-length 0
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95 --min-alternate-count 1
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96 --min-alternate-fraction 0.05
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97 --pooled-continuous
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98 --report-monomorphic
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99 #elif str( $options_type.options_type_selector ) == "naive_w_filters":
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100 --haplotype-length 0
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101 --min-alternate-count 1
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102 --min-alternate-fraction 0.05
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103 --pooled-continuous
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104 --report-monomorphic
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105 --standard-filters
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106 #elif str( $options_type.options_type_selector ) == "full":
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107 #if str( $options_type.optional_inputs.optional_inputs_selector ) == 'set':
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108 ${options_type.optional_inputs.report_monomorphic}
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109
6
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110 #if $options_type.optional_inputs.output_trace_option:
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111 --trace ./trace/part_'\$i'.txt
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112 #end if
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113 #if $options_type.optional_inputs.output_failed_alleles_option:
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114 --failed-alleles ./failed_alleles/part_'\$i'.bed
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115 #end if
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116 #if $options_type.optional_inputs.samples:
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117 --samples '${options_type.optional_inputs.samples}'
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118 #end if
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119 #if $options_type.optional_inputs.populations:
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120 --populations '${options_type.optional_inputs.populations}'
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121 #end if
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122 #if $options_type.optional_inputs.A:
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123 --cnv-map '${options_type.optional_inputs.A}'
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124 #end if
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125 #if str( $options_type.optional_inputs.input_variant_type.input_variant_type_selector ) == "provide_vcf":
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126 --variant-input 'input_variant_vcf.vcf.gz' ## input_variant_vcf.vcf.gz is symlinked to a galaxy-generated dataset in "Tabixize optional input_variant_vcf file" section of the command line above
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127 ${options_type.optional_inputs.input_variant_type.only_use_input_alleles}
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128 #end if
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129 #if $options_type.optional_inputs.haplotype_basis_alleles:
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130 --haplotype-basis-alleles '${options_type.optional_inputs.haplotype_basis_alleles}'
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131 #end if
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132 #if $options_type.optional_inputs.observation_bias:
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133 --observation-bias '${options_type.optional_inputs.observation_bias}'
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134 #end if
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135 #if $options_type.optional_inputs.contamination_estimates:
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136 --contamination-estimates '${options_type.optional_inputs.contamination_estimates}'
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137 #end if
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138 #end if
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139
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140 ## REPORTING
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141 #if str( $options_type.reporting.reporting_selector ) == "set":
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142 --pvar ${options_type.reporting.pvar}
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143 #end if
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144 ## POPULATION MODEL
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145 #if str( $options_type.population_model.population_model_selector ) == "set":
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146 --theta ${options_type.population_model.T}
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147 --ploidy ${options_type.population_model.P}
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148 ${options_type.population_model.J}
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149 ${options_type.population_model.K}
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150 #end if
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151
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152 ## REFERENCE ALLELE
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153 #if str( $options_type.reference_allele.reference_allele_selector ) == "set":
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154 ${options_type.reference_allele.Z}
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155 --reference-quality '${options_type.reference_allele.reference_quality}'
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156 #end if
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157
6
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158 ## ALLELE SCOPE
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159 #if str( $options_type.allele_scope.allele_scope_selector ) == "set":
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160 ${options_type.allele_scope.I}
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161 ${options_type.allele_scope.i}
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162 ${options_type.allele_scope.X}
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163 ${options_type.allele_scope.u}
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164 ${options_type.allele_scope.no_partial_observations}
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165
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166 -n ${options_type.allele_scope.n}
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167
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168 --haplotype-length ${options_type.allele_scope.haplotype_length}
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169 --min-repeat-size ${options_type.allele_scope.min_repeat_length}
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170 --min-repeat-entropy ${options_type.allele_scope.min_repeat_entropy}
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171 #end if
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172
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173 ## REALIGNMENT
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174 ${options_type.O}
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175
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176 ##INPUT FILTERS
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177 #if str( $options_type.input_filters.input_filters_selector ) == "set":
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178 ${options_type.input_filters.use_duplicate_reads}
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179 -m ${options_type.input_filters.m}
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180 -q ${options_type.input_filters.q}
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181 -R ${options_type.input_filters.R}
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182 -Y ${options_type.input_filters.Y}
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183 -e ${options_type.input_filters.e}
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184 -F ${options_type.input_filters.F}
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185 -C ${options_type.input_filters.C}
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186 -G ${options_type.input_filters.G}
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187
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188 #if str( $options_type.input_filters.mismatch_filters.mismatch_filters_selector ) == "set":
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189 -Q ${options_type.input_filters.mismatch_filters.Q}
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190 #if str($options_type.input_filters.mismatch_filters.U)
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191 -U ${options_type.input_filters.mismatch_filters.U}
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192 #end if
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193 -z ${options_type.input_filters.mismatch_filters.z}
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194
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195 --read-snp-limit ${options_type.input_filters.mismatch_filters.read_snp_limit}
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196 #end if
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197
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198 --min-alternate-qsum ${options_type.input_filters.min_alternate_qsum}
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199 #end if
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200
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201 ## POPULATION AND MAPPABILITY PRIORS
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202 #if str( $options_type.population_mappability_priors.population_mappability_priors_selector ) == "set":
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203 ${options_type.population_mappability_priors.k}
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204 ${options_type.population_mappability_priors.w}
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205 ${options_type.population_mappability_priors.V}
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206 ${options_type.population_mappability_priors.a}
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207 #end if
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208
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209 ## GENOTYPE LIKELIHOODS
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210 #if str( $options_type.genotype_likelihoods.genotype_likelihoods_selector ) == "set":
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211 ${$options_type.genotype_likelihoods.experimental_gls}
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212
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213 --base-quality-cap ${$options_type.genotype_likelihoods.base_quality_cap}
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214 --prob-contamination ${$options_type.genotype_likelihoods.prob_contamination}
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215 #end if
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216
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217 ## ALGORITHMIC FEATURES
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218 #if str( $options_type.algorithmic_features.algorithmic_features_selector ) == "set":
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219 -B '${options_type.algorithmic_features.B}'
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220 -W '${options_type.algorithmic_features.W}'
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221 -D '${options_type.algorithmic_features.D}'
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222
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223 #if str($options_type.algorithmic_features.genotype_variant_threshold)
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224 -S ${options_type.algorithmic_features.genotype_variant_threshold}
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225 #end if
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226
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227 ${options_type.algorithmic_features.N}
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228 ${options_type.algorithmic_features.j}
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229 ${options_type.algorithmic_features.H}
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230 ${options_type.algorithmic_features.genotype_qualities}
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231 ${options_type.algorithmic_features.report_genotype_likelihood_max}
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232
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233 --genotyping-max-banddepth ${options_type.algorithmic_features.genotyping_max_banddepth}
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234 #end if
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235 #end if
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236
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237 ";
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238 done > freebayes_commands.sh &&
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239
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240 cat freebayes_commands.sh |
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241 parallel --will-cite -j \${GALAXY_SLOTS:-1} &&
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242
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243 ## make VCF header
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244 grep "^#" "./vcf_output/part_\$i.vcf" > header.txt &&
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245
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246 for i in `cat regions_uniq.bed | awk '{print $1":"$2".."$3}'`;
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247 do
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248 ## if this fails then it bails out the script
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249 cat "./vcf_output/part_\$i.vcf" | grep -v "^#" || true
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250 ;
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251 done | sort -k1,1 -k2,2n -k5,5 -u | cat header.txt - > '${output_vcf}'
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252
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253 #if str( $options_type.options_type_selector ) == "full":
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254 #if str( $options_type.optional_inputs.optional_inputs_selector ) == 'set':
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255 #if $options_type.optional_inputs.output_failed_alleles_option:
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256 &&
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257 for i in `cat regions.bed | awk '{print $1":"$2".."$3}'`;
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258 do
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259 cat "./failed_alleles/part_\$i.bed"
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260 ;
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261 done > '${output_failed_alleles_bed}'
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262 #end if
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263
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264 #if $options_type.optional_inputs.output_trace_option:
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265 &&
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266 for i in `cat regions.bed | awk '{print $1":"$2".."$3}'`;
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267 do
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268 cat './trace/part_\$i.txt'
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269 ;
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270 done > '${output_trace}'
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271 #end if
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272 #end if
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273 #end if
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274 ]]></command>
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275
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276 <inputs>
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277 <conditional name="reference_source">
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278 <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">
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279 <option value="cached">Locally cached</option>
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280 <option value="history">History</option>
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281 </param>
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282 <when value="cached">
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283 <expand macro="input_bam">
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284 <expand macro="validation" />
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285 </expand>
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286 <param name="ref_file" type="select" label="Using reference genome">
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287 <options from_data_table="fasta_indexes" />
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288 <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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289 </param>
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290 </when>
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291 <when value="history"> <!-- FIX ME!!!! -->
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292 <expand macro="input_bam" />
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293 <param name="ref_file" type="data" format="fasta" label="Use the following dataset as the reference sequence"
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294 help="You can upload a FASTA sequence to the history and use it as reference" />
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295 </when>
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296 </conditional>
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297 <conditional name="target_limit_type">
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298 <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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299 <option value="do_not_limit" selected="true">Do not limit</option>
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300 <option value="limit_by_target_file">Limit by target file</option>
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301 <option value="limit_by_region">Limit to region</option>
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302 </param>
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303 <when value="do_not_limit" />
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304 <when value="limit_by_target_file">
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305 <param name="input_target_bed" argument="--targets" type="data" format="bed" label="Limit analysis to regions in this BED dataset" />
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306 </when>
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307 <when value="limit_by_region">
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308 <param name="region_chromosome" argument="--region" type="text" label="Region Chromosome" value="" /> <!--only once? -->
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309 <param name="region_start" type="integer" label="Region Start" value="" />
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310 <param name="region_end" type="integer" label="Region End" value="" />
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311 </when>
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312 </conditional>
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313 <conditional name="coverage_options">
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314 <param name="coverage_options_selector" type="select" label="Read coverage"
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315 help="Sets --min-coverage, --limit-coverage, and --skip-coverage">
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316 <option value="do_not_set" selected="true">Use defaults</option>
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317 <option value="set">Specify coverage options</option>
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318 </param>
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319 <when value="set">
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320 <expand macro="par_min_cov" />
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321 </when>
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322 <when value="do_not_set" />
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323 </conditional>
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324 <conditional name="options_type">
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325 <param name="options_type_selector" type="select" label="Choose parameter selection level"
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326 help="Select how much control over the freebayes run you need">
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327 <option value="simple" selected="true">1. Simple diploid calling</option>
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328 <option value="simple_w_filters">2. Simple diploid calling with filtering and coverage</option>
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329 <option value="naive">3. Frequency-based pooled calling</option>
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330 <option value="naive_w_filters">4. Frequency-based pooled calling with filtering and coverage</option>
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331 <option value="full">5. Full list of options</option>
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332 </param>
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333 <when value="full">
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334
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335 <conditional name="optional_inputs">
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336 <param name="optional_inputs_selector" type="select" label="Additional inputs"
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337 help="Sets --samples, --populations, --cnv-map, --trace, --failed-alleles, --variant-input, --only-use-input-alleles, --haplotype-basis-alleles, --report-all-haplotype-alleles, --report-monomorphic options, --observation-bias, and --contamination-estimates">
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338 <option value="do_not_set" selected="true">Do not provide additional inputs</option>
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339 <option value="set">Provide additional inputs</option>
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340 </param>
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341 <when value="set">
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342 <param name="output_failed_alleles_option" argument="--failed-alleles" type="boolean" truevalue="--failed-alleles" falsevalue="" checked="false"
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343 label="Write out failed alleles file" />
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344 <param name="output_trace_option" argument="--trace" type="boolean" truevalue="--trace" falsevalue="" checked="false"
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345 label="Write out algorithm trace file" />
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346 <param argument="--samples" type="data" format="txt"
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347 label="Limit analysis to samples listed (one per line) in this dataset" optional="true"
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348 help="By default FreeBayes will analyze all samples in its input BAM datasets" />
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349 <param argument="--populations" type="data" format="txt" optional="true"
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350 label="Populations dataset"
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351 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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352 <param name="A" argument="--cnv-map" type="data" format="bed" optional="true"
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353 label="Read a copy number map from a BED dataset"
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354 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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355 <conditional name="input_variant_type">
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356 <param name="input_variant_type_selector" type="select" label="Provide variants dataset">
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357 <option value="do_not_provide" selected="true">Do not provide</option>
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358 <option value="provide_vcf">Provide VCF dataset</option>
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359 </param>
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360 <when value="do_not_provide" />
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361 <when value="provide_vcf">
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362 <param name="input_variant_vcf" argument="--variant-input" type="data" format="vcf_bgzip"
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363 label="Use variants reported in this VCF dataset as input to the algorithm">
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364 <conversion name="Tabixized_input" type="tabix" />
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365 </param>
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366 <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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367 label="Only provide variant calls and genotype likelihoods for sites in VCF" />
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368 </when>
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369 </conditional>
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370 <param name="haplotype_basis_alleles" argument="--haplotype-basis-alleles" type="data" format="vcf" optional="true"
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371 label="Only use variant alleles provided in this input VCF for the construction of complex or haplotype alleles" />
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372 <param name="report_monomorphic" argument="--report-monomorphic" type="boolean" truevalue="--report-monomorphic" falsevalue="" checked="false"
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373 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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374 <param name="observation_bias" argument="--observation-bias" type="data" format="tabular" optional="true"
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375 label="Load read length-dependent allele observation biases from"
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376 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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377 <param name="contamination_estimates" argument="--contamination-estimates" type="data" format="tabular" optional="true"
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378 label="Upload per-sample estimates of contamination from"
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379 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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380 </when>
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381 <when value="do_not_set" />
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382 </conditional>
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383
4
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384 <!-- reporting -->
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385 <conditional name="reporting">
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386 <param name="reporting_selector" type="select" label="Reporting options" help="Sets -P --pvar option">
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387 <option value="do_not_set" selected="true">Use defaults</option>
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388 <option value="set">Set reporting options</option>
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389 </param>
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390 <when value="set">
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391 <param argument="--pvar" type="float" value="0.0"
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392 label="Report sites if the probability that there is a polymorphism at the site is greater than"
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393 help="Note that post-filtering is generally recommended over the use of this parameter" />
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394 </when>
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395 <when value="do_not_set" />
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396 </conditional>
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397
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398 <!-- population model -->
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399 <conditional name="population_model">
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400 <param name="population_model_selector" type="select" label="Population model options"
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401 help="Sets --theta, --ploidy, --pooled-discrete, and --pooled-continuous options">
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402 <option value="do_not_set" selected="true">Use defaults</option>
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403 <option value="set">Set population model options</option>
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404 </param>
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405 <when value="set">
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406 <param name="T" argument="--theta" type="float" value="0.001"
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407 label="The expected mutation rate or pairwise nucleotide diversity among the population under analysis"
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408 help="This serves as the single parameter to the Ewens Sampling Formula prior model" />
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409 <param name="P" argument="--ploidy" type="integer" value="2"
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410 label="Set ploidy for the analysis" />
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411 <param name="J" argument="--pooled-discrete" type="boolean" truevalue="-J" falsevalue="" checked="false"
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412 label="Assume that samples result from pooled sequencing"
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413 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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414 <param name="K" argument="--poled-continuous" type="boolean" truevalue="-K" falsevalue="" checked="false"
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415 label="Output all alleles which pass input filters, regardles of genotyping outcome or model" />
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416 </when>
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417 <when value="do_not_set" />
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418 </conditional>
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419
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420 <!-- reference allele -->
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421 <conditional name="reference_allele">
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422 <param name="reference_allele_selector" type="select" label="Reference allele options"
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423 help="Sets --use-reference-allele and --reference-quality options">
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424 <option value="do_not_set" selected="true">Use defaults</option>
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425 <option value="set">Set reference allele options</option>
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426 </param>
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427 <when value="set">
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428 <param name="Z" argument="--use-reference-allele" type="boolean" truevalue="-Z" falsevalue="" checked="false"
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429 label="Include the reference allele in the analysis as if it is another sample from the same population" />
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430 <param name="reference_quality" argument="--reference-quality" type="text" value="100,60"
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431 label="Assign mapping quality of MQ (100) to the reference allele at each site and base quality of BQ (60)" />
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432 </when>
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433 <when value="do_not_set" />
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434 </conditional>
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435
4
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diff changeset
436 <!-- allelic scope -->
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diff changeset
437 <conditional name="allele_scope">
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438 <param name="allele_scope_selector" type="select" label="Allelic scope options"
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parents: 8
diff changeset
439 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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440 <option value="do_not_set" selected="true">Use defaults</option>
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parents: 3
diff changeset
441 <option value="set">Set alleic scope options</option>
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parents: 3
diff changeset
442 </param>
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443 <when value="set">
9
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parents: 8
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444 <param name="I" argument="--no-snps" type="boolean" truevalue="-I" 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
445 label="Ignore SNP alleles" />
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
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parents: 8
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446 <param name="i" argument="--no-indels" type="boolean" truevalue="-i" 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
447 label="Ignore indels alleles" />
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
448 <param name="X" argument="--no-mnps" type="boolean" truevalue="-X" falsevalue="" checked="false"
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parents: 8
diff changeset
449 label="Ignore multi-nucleotide polymorphisms, MNPs" />
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
450 <param name="u" argument="--no-complex" type="boolean" truevalue="-u" 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
451 label="Ignore complex events (composites of other classes)" />
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
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parents: 8
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452 <param name="n" argument="--use-best-n-alleles" type="integer" value="0"
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
453 label="How many best SNP alleles to evaluate"
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parents: 8
diff changeset
454 help="Alleles are ranked by the sum of supporting quality scores. Set to 0 to evaluate all" />
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
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parents: 8
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455 <param name="haplotype_length" argument="--haplotype-length" type="integer" value="3"
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
456 label="Allow haplotype calls with contiguous embedded matches of up to (nucleotides)" />
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
457 <param name="min_repeat_length" argument="--min-repeat-size" type="integer" value="5"
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
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parents: 8
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458 label="When assembling observations across repeats, require the total repeat length at least this many bp" />
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parents: 10
diff changeset
459 <param name="min_repeat_entropy" argument="--min-repeat-entropy" type="integer" value="1"
9
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parents: 8
diff changeset
460 label="To detect interrupted repeats, build across sequence until it has entropy > (bits per bp)" />
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parents: 8
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461 <param name="no_partial_observations" argument="--no-partial-observations" type="boolean" truevalue="--no-partial-observations" falsevalue="" checked="false"
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parents: 5
diff changeset
462 label="Exclude observations which do not fully span the dynamically-determined detection window"
9
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parents: 8
diff changeset
463 help="By default, FreeBayes uses all observations, dividing partial support across matching haplotypes when generating haplotypes" />
4
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parents: 3
diff changeset
464 </when>
9
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parents: 8
diff changeset
465 <when value="do_not_set" />
4
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diff changeset
466 </conditional>
6
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parents: 5
diff changeset
467
4
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parents: 3
diff changeset
468 <!-- indel realignment -->
9
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parents: 8
diff changeset
469 <param name="O" argument="--dont-left-align-indels" type="boolean" truevalue="-O" falsevalue="" checked="false"
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parents: 8
diff changeset
470 label="Turn off left-alignment of indels" />
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parents: 5
diff changeset
471
4
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parents: 3
diff changeset
472 <!-- input filters -->
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parents: 3
diff changeset
473 <conditional name="input_filters">
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parents: 3
diff changeset
474 <param name="input_filters_selector" type="select" label="Input filters"
9
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parents: 8
diff changeset
475 help="Sets -4, -m, -q, -R, -Y, -Q, -U, -z, -&#36;, -e, -0, -F, -C, -3, -G, and -&#33; options">
4
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diff changeset
476 <option value="do_not_set" selected="true">No input filters (default)</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
477 <option value="set">Set input filters</option>
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parents: 3
diff changeset
478 </param>
6
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parents: 5
diff changeset
479 <when value="set">
9
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parents: 8
diff changeset
480 <param name="use_duplicate_reads" argument="--use-duplicate-reads" type="boolean" truevalue="--use-duplicate-reads" 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
481 label="Include duplicate-marked alignments in the analysis" />
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
482 <param name="m" argument="--min-mapping-quality" type="integer" value="1"
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
483 label="Exclude alignments from analysis if they have a mapping quality less than" />
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
484 <param name="q" argument="--min-base-quality" 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
485 label="Exclude alleles from analysis if their supporting base quality less than" />
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
486 <param name="R" argument="--min-supporting-allele-qsum" type="integer" value="0"
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
487 label="Consider any allele in which the sum of qualities of supporting observations is at least" />
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
488 <param name="Y" argument="--min-supporting-mapping-qsum" type="integer" value="0"
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
489 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
490 <conditional name="mismatch_filters">
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parents: 3
diff changeset
491 <param name="mismatch_filters_selector" type="select" label="Mismatch filters"
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parents: 5
diff changeset
492 help="Sets -Q, -U, -z, and &#36; options">
4
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parents: 3
diff changeset
493 <option value="do_not_set" selected="true">No mismatch filters (default)</option>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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parents: 3
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494 <option value="set">Set mismatch filters</option>
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parents: 3
diff changeset
495 </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
496 <when value="set">
9
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parents: 8
diff changeset
497 <param name="Q" argument="--mismatch-base-quality-threshold" type="integer" value="10"
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
498 label="Count mismatches toward -U (option below) if the base quality of the mismatch is >=" />
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
499 <param name="U" type="integer" argument="--read-mismatch-limit" value="1000" optional="true"
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
500 label="Exclude reads with more than N mismatches where each mismatch has base quality >= mismatch-base-quality-threshold (option above)"
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
501 help="default=~unbounded" />
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
502 <param name="z" argument="--read-max-mismatch-fraction" type="float" value="1.0" min="0.0" max="1.0"
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
503 label="Exclude reads with more than N [0,1] fraction of mismatches where each mismatch has base quality >= mismatch-base-quality-threshold (second option above)" />
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
504 <param name="read_snp_limit" argument="--read-snp-limit" 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
505 label="Exclude reads with more than N base mismatches, ignoring gaps with quality >= mismatch-base-quality-threshold (third option above)"
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
506 help="default=~unbounded" />
4
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parents: 3
diff changeset
507 </when>
9
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parents: 8
diff changeset
508 <when value="do_not_set" />
4
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diff changeset
509 </conditional>
9
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parents: 8
diff changeset
510 <param name="e" argument="--read-indel-limit" 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
511 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
512 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
513 <param name="standard_filters" argument="--standard-filters" type="boolean" truevalue="-0" falsevalue="" checked="false"
6
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parents: 5
diff changeset
514 label="Use stringent input base and mapping quality filters"
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
515 help="Equivalent to -m 30 -q 20 -R 0 -S 0" />
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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
516 <param name="F" argument="--min-alternate-fraction" type="float" value="0.05"
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
517 label="Require at least this fraction of observations supporting an alternate allele within a single individual in the in order to evaluate the position" />
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
518 <param name="C" argument="--min-alternate-count" type="integer" value="2"
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
519 label="Require at least this count of observations supporting an alternate allele within a single individual in order to evaluate the position" />
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
520 <param name="min_alternate_qsum" argument="--min-alternate-qsum" 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
521 label="Require at least this sum of quality of observations supporting an alternate allele within a single individual in order to evaluate the position" />
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
522 <param name="G" argument="--min-alternate-total" type="integer" value="1"
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
523 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
524 </when>
9
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iuc
parents: 8
diff changeset
525 <when value="do_not_set" />
4
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parents: 3
diff changeset
526 </conditional>
6
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iuc
parents: 5
diff changeset
527
4
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parents: 3
diff changeset
528 <!-- population and mappability priors -->
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
529 <conditional name="population_mappability_priors">
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
530 <param name="population_mappability_priors_selector" type="select" label="Population and mappability priors"
9
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iuc
parents: 8
diff changeset
531 help="Sets -k, -w, -V, and -a options">
4
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parents: 3
diff changeset
532 <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
533 <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
534 </param>
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parents: 3
diff changeset
535 <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
536 <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
iuc
parents: 8
diff changeset
537 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
538 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
539 <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
540 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
541 <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
542 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
543 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
544 <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
545 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
546 </when>
9
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parents: 8
diff changeset
547 <when value="do_not_set" />
4
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parents: 3
diff changeset
548 </conditional>
6
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iuc
parents: 5
diff changeset
549
4
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parents: 3
diff changeset
550 <!-- 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
551 <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
552 <param name="genotype_likelihoods_selector" type="select" label="Genotype likelihood options"
9
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iuc
parents: 8
diff changeset
553 help="Sets --base-quality-cap, --experimental-gls, and --prob-contamination options">
4
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parents: 3
diff changeset
554 <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
555 <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
556 </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
557 <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
558 <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
559 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
560 <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
561 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
562 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
563 <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
564 label="An estimate of contamination to use for all samples" />
4
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parents: 3
diff changeset
565 </when>
9
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
566 <when value="do_not_set" />
4
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devteam
parents: 3
diff changeset
567 </conditional>
6
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iuc
parents: 5
diff changeset
568
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
569 <!-- algorithmic features -->
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
570 <conditional name="algorithmic_features">
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
571 <param name="algorithmic_features_selector" type="select" label="Algorithmic features"
6
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iuc
parents: 5
diff changeset
572 help="Sets --report-genotypes-likelihood-max, -B, --genotyping-max-banddepth, -W, -N, S, -j, -H, -D, -= options">
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
573 <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
574 <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
575 </param>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
576 <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
577 <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
578 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
579 <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
580 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
581 <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
582 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
583 <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
584 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
585 <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
586 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
587 <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
588 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
589 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
590 <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
591 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
592 <param name="H" argument="--harmonic-indel-quality" type="boolean" truevalue="-H" falsevalue="" checked="false"
6
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iuc
parents: 5
diff changeset
593 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
594 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
595 <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
596 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
597 <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
598 label="Calculate the marginal probability of genotypes and report as GQ in each sample field in the VCF output" />
4
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parents: 3
diff changeset
599 </when>
9
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
600 <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
601 </conditional>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
602 </when>
9
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
603 <when value="simple" />
11
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
604 <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
605 <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
606 <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
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 </inputs>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
609 <outputs>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
610 <data format="vcf" name="output_vcf" label="${tool.name} on ${on_string} (variants)" />
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
611 <data format="bed" name="output_failed_alleles_bed" label="${tool.name} on ${on_string} (failed alleles)">
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
612 <filter>( options_type['options_type_selector'] == 'cline' or options_type['options_type_selector'] == 'full' ) and options_type['optional_inputs']['optional_inputs_selector'] == 'set' and options_type['optional_inputs']['output_failed_alleles_option'] is True</filter>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
613 </data>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
614 <data format="txt" name="output_trace" label="${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
615 <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
616 </data>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
617 </outputs>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
618 <tests>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
619 <test>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
620 <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
621 <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
622 <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
623 <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
624 <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
625 <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
626 </test>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
627 <test>
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="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
629 <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
630 <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
631 <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
632 <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
633 <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
634 <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
635 <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
636 </test>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
637 <test>
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="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
639 <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
640 <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
641 <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
642 <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
643 <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
644 <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
645 <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
646 </test>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
647 <test>
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="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
649 <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
650 <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
651 <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
652 <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
653 <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
654 <param name="P" value="1"/>
10
2fb16f415220 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 99e8a87a2993ae644df15756044a40a42aa7a05b
iuc
parents: 9
diff changeset
655 <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
656 </test>
11
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
657 <test>
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
658 <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
659 <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
660 <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
661 <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
662 <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
663 <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
664 <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
665 <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
666 </test>
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
667 <test>
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="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
669 <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
670 <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
671 <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
672 <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
673 <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
674 <param name="limit_coverage" value="400" />
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
675 <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"
iuc
parents: 10
diff changeset
676 </test>
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
677 <test>
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="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
679 <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
680 <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
681 <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
682 <param name="options_type_selector" value="simple"/>
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683 <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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684 <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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685 <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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686 </test>
4
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687 </tests>
11
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688 <help><![CDATA[
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689 **What it does**
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690
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691 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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692
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693 See https://github.com/ekg/freebayes for details on FreeBayes.
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694
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695 ------
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696
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697 **Description**
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698
9
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
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699 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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700
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701 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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702
2
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703 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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704
2
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705 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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706
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707 FreeBayes can act as a frequency-based pooled caller and describe variants and haplotypes in terms of observation frequency rather than called genotypes. To do so, use --pooled-continuous and set input filters to a suitable level. Allele observation counts will be described by AO and RO fields in the VCF output.
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708
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709 -------
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710
2
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711 **Galaxy-specific options**
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712
9
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
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713 Galaxy allows five levels of control over FreeBayes options, provided by the **Choose parameter selection level** menu option. These are:
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714
9
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715 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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716 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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717 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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718 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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719 5. *Complete list of all options*: Gives you full control by exposing all FreeBayes options as Galaxy parameters.
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720
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721 ------
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722
11
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diff changeset
723 **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
724
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
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diff changeset
725 **Input**::
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
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726
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727 --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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728 --bam-list FILE A file containing a list of BAM files to be analyzed.
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diff changeset
729
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
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730 --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
731 --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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732 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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733 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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734 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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735 --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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diff changeset
736 --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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diff changeset
737 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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diff changeset
738 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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diff changeset
739 --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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740 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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741 BAM files.
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
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742 --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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diff changeset
743 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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diff changeset
744 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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745 --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
746 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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diff changeset
747 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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748 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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749 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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750 ... 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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751 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
752 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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753
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754 **Output**::
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
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755
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756 --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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757 --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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758 --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
759 --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"
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diff changeset
760 set to "true" , will also route an int to --gvcf-chunk
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diff changeset
761 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"
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762 --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"
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diff changeset
763 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"
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764 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"
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765 --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"
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766 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"
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diff changeset
767 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"
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diff changeset
768 have support in the data.
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
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diff changeset
769 --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"
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diff changeset
770 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"
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diff changeset
771 alleles.
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
772 --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"
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parents: 10
diff changeset
773 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"
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parents: 10
diff changeset
774 those which are called.
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
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775 --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"
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diff changeset
776 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"
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777 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"
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diff changeset
778 --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
779 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
780 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
781 --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
782
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
783 **Population model**::
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
784
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
785 --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
786 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
787 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
788 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
789 --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
790 --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
791 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
792 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
793 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
794 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
795 --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
796 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
797
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
798 **Reference allele**::
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 --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
801 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
802 --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
803 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
804
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
805 **Allele scope**::
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
806
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
807 --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
808 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
809 --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
810 --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
811 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
812 --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
813 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
814 --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
815 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
816 --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
817 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
818 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
819
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
820 **Indel realignment**::
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 --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
823
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
824 **Input filters**::
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
825
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
826 --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
827 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
828 --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
829 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
830 --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
831 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
832 --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
833 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
834 --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
835 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
836 --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
837 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
838 --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
839 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
840 default: ~unbounded
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
841 --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
842 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
843 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
844 --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
845 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
846 default: ~unbounded
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
847 --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
848 default: ~unbounded
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
849 --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
850 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
851 --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
852 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
853 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
854 --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
855 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
856 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
857 --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
858 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
859 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
860 --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
861 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
862 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
863 --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
864 --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
865 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
866 --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
867 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
868 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
869
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
870 **Population priors**::
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
871
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
872 --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
873 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
874
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
875 **Mappability priors**::
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
876
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
877 --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
878 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
879 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
880 --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
881 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
882 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
883 --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
884 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
885
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
886 **Genotype likelihoods**::
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
887
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
888 --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
889 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
890 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
891 --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
892 --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
893 --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
894 --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
895 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
896 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
897 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
898
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
899 **Algorithmic features**::
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 --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
902 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
903 --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
904 --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
905 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
906 --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
907 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
908 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
909 --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
910 --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
911 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
912 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
913 --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
914 --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
915 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
916 --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
917 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
918 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
919 --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
920 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
921
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
922 ------
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
923
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
924 **Acknowledgments**
0
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
925
2
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
926 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
927 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
928 ]]>
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
929 </help>
10
2fb16f415220 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 99e8a87a2993ae644df15756044a40a42aa7a05b
iuc
parents: 9
diff changeset
930 <expand macro="citations">
2fb16f415220 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 99e8a87a2993ae644df15756044a40a42aa7a05b
iuc
parents: 9
diff changeset
931 <citation type="bibtex">
2fb16f415220 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 99e8a87a2993ae644df15756044a40a42aa7a05b
iuc
parents: 9
diff changeset
932 @article{Tange2011a,
2fb16f415220 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 99e8a87a2993ae644df15756044a40a42aa7a05b
iuc
parents: 9
diff changeset
933 title = {GNU Parallel - The Command-Line Power Tool},
2fb16f415220 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 99e8a87a2993ae644df15756044a40a42aa7a05b
iuc
parents: 9
diff changeset
934 author = {O. Tange},
2fb16f415220 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 99e8a87a2993ae644df15756044a40a42aa7a05b
iuc
parents: 9
diff changeset
935 address = {Frederiksberg, Denmark},
2fb16f415220 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 99e8a87a2993ae644df15756044a40a42aa7a05b
iuc
parents: 9
diff changeset
936 journal = {;login: The USENIX Magazine},
2fb16f415220 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 99e8a87a2993ae644df15756044a40a42aa7a05b
iuc
parents: 9
diff changeset
937 month = {Feb},
2fb16f415220 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 99e8a87a2993ae644df15756044a40a42aa7a05b
iuc
parents: 9
diff changeset
938 number = {1},
2fb16f415220 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 99e8a87a2993ae644df15756044a40a42aa7a05b
iuc
parents: 9
diff changeset
939 volume = {36},
2fb16f415220 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 99e8a87a2993ae644df15756044a40a42aa7a05b
iuc
parents: 9
diff changeset
940 url = {http://www.gnu.org/s/parallel},
2fb16f415220 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 99e8a87a2993ae644df15756044a40a42aa7a05b
iuc
parents: 9
diff changeset
941 year = {2011},
2fb16f415220 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 99e8a87a2993ae644df15756044a40a42aa7a05b
iuc
parents: 9
diff changeset
942 pages = {42-47}
2fb16f415220 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 99e8a87a2993ae644df15756044a40a42aa7a05b
iuc
parents: 9
diff changeset
943 }
2fb16f415220 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 99e8a87a2993ae644df15756044a40a42aa7a05b
iuc
parents: 9
diff changeset
944 </citation>
2fb16f415220 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 99e8a87a2993ae644df15756044a40a42aa7a05b
iuc
parents: 9
diff changeset
945 </expand>
0
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
946 </tool>