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annotate freebayes.xml @ 11:f14331392369 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
author iuc
date Wed, 06 Nov 2019 17:02:36 -0500
parents 2fb16f415220
children 2667d6a97b50
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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 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements">
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7 <requirement type="package" version="4.1.3">gawk</requirement>
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8 <requirement type="package" version="20170422">parallel</requirement>
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9 </expand>
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
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10 <command detect_errors="exit_code"><![CDATA[
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11 ##set up input files
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12
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13 #set $reference_fasta_filename = "localref.fa"
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14
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15 #if str( $reference_source.reference_source_selector ) == "history":
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16 ln -s -f '${reference_source.ref_file}' '${reference_fasta_filename}' &&
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
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17 samtools faidx '${reference_fasta_filename}' 2>&1 || echo "Error running samtools faidx for FreeBayes" >&2 &&
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18 #else:
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19 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
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20 #end if
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21
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22 #if $reference_source.batchmode.processmode == 'merge':
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23 #set $input_bamfiles = $reference_source.batchmode.input_bams
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24 #else:
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25 #set $input_bamfiles = [ $reference_source.batchmode.input_bams ]
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26 #end if
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28 #for $bam_count, $input_bam in enumerate( $input_bamfiles ):
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29 ln -s -f '${input_bam}' 'b_${bam_count}.bam' &&
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
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30 ln -s -f '${input_bam.metadata.bam_index}' 'b_${bam_count}.bam.bai' &&
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31 #end for
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32
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33 ## Tabixize optional input_variant_vcf file (for --variant-input option)
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34 #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( $options_type.optional_inputs.input_variant_type.input_variant_type_selector ) == "provide_vcf":
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c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
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35 ln -s -f '${options_type.optional_inputs.input_variant_type.input_variant_vcf}' input_variant_vcf.vcf.gz &&
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36 ln -s -f '${Tabixized_input}' input_variant_vcf.vcf.gz.tbi &&
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37 #end if
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38
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39 ##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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40 #if str( $target_limit_type.target_limit_type_selector ) == "limit_by_target_file":
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41 ln -s '${target_limit_type.input_target_bed}' regions_all.bed &&
d0997bd93c49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 0c59a0b32e4875120e697951a187b81c662bc39c
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42 #elif str( $target_limit_type.target_limit_type_selector ) == "limit_by_region":
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43 printf '${target_limit_type.region_chromosome}\t${target_limit_type.region_start}\t${target_limit_type.region_end}' > regions_all.bed &&
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44 #else
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45 ##divide up the regions in the bam file for efficient processing
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46 #for $bam_count, $input_bam in enumerate( $input_bamfiles ):
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47 samtools view -H b_${bam_count}.bam |
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48 grep '^@SQ' |
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49 cut -f 2- |
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50 awk '{ gsub("^SN:","",$1); gsub("^LN:","",$2); print $1"\t0\t"$2; }' >> regions_all.bed &&
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51 #end for
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52 #end if
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53
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54 sort -u regions_all.bed > regions_uniq.bed &&
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55 ## split into even small chunks, this has some disatvantages and will not be used for the moment
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56 ## bedtools makewindows -b regions_uniq.bed -w 10000000 -s 9990000 > regions.bed &&
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57
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58 mkdir vcf_output failed_alleles trace &&
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60 ## Finished setting up inputs
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62 for i in `cat regions_uniq.bed | awk '{print $1":"$2".."$3}'`;
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63 do
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64 echo "
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65
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66 ## COMMAND LINE STARTS HERE
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67
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68 freebayes
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69
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70 --region '\$i'
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71
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72 #for $bam_count, $input_bam in enumerate( $input_bamfiles ):
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73 --bam 'b_${bam_count}.bam'
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74 #end for
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75 --fasta-reference '${reference_fasta_filename}'
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76
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77 ## Outputs
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78 --vcf './vcf_output/part_\$i.vcf'
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79
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80 ## Coverage
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
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81 #if str($coverage_options.coverage_options_selector) == "set":
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82 @COVERAGE@
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83 #end if
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84
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85 ##advanced options
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86 #if str( $options_type.options_type_selector ) == "simple":
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87 #pass
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88 #elif str( $options_type.options_type_selector ) == "simple_w_filters":
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89 --standard-filters
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90 #elif str( $options_type.options_type_selector ) == "naive":
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91 --haplotype-length 0
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92 --min-alternate-count 1
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93 --min-alternate-fraction 0.05
6
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94 --pooled-continuous
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95 --report-monomorphic
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96 #elif str( $options_type.options_type_selector ) == "naive_w_filters":
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97 --haplotype-length 0
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98 --min-alternate-count 1
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99 --min-alternate-fraction 0.05
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100 --pooled-continuous
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101 --report-monomorphic
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102 --standard-filters
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103 #elif str( $options_type.options_type_selector ) == "full":
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104 #if str( $options_type.optional_inputs.optional_inputs_selector ) == 'set':
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105 ${options_type.optional_inputs.report_monomorphic}
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106
6
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107 #if $options_type.optional_inputs.output_trace_option:
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108 --trace ./trace/part_'\$i'.txt
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109 #end if
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110 #if $options_type.optional_inputs.output_failed_alleles_option:
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111 --failed-alleles ./failed_alleles/part_'\$i'.bed
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112 #end if
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113 #if $options_type.optional_inputs.samples:
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114 --samples '${options_type.optional_inputs.samples}'
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115 #end if
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116 #if $options_type.optional_inputs.populations:
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117 --populations '${options_type.optional_inputs.populations}'
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118 #end if
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119 #if $options_type.optional_inputs.A:
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120 --cnv-map '${options_type.optional_inputs.A}'
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121 #end if
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122 #if str( $options_type.optional_inputs.input_variant_type.input_variant_type_selector ) == "provide_vcf":
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123 --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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124 ${options_type.optional_inputs.input_variant_type.only_use_input_alleles}
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125 #end if
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126 #if $options_type.optional_inputs.haplotype_basis_alleles:
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127 --haplotype-basis-alleles '${options_type.optional_inputs.haplotype_basis_alleles}'
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128 #end if
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129 #if $options_type.optional_inputs.observation_bias:
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130 --observation-bias '${options_type.optional_inputs.observation_bias}'
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131 #end if
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132 #if $options_type.optional_inputs.contamination_estimates:
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133 --contamination-estimates '${options_type.optional_inputs.contamination_estimates}'
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134 #end if
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135 #end if
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136
6
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137 ## REPORTING
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138 #if str( $options_type.reporting.reporting_selector ) == "set":
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139 --pvar ${options_type.reporting.pvar}
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140 #end if
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141 ## POPULATION MODEL
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142 #if str( $options_type.population_model.population_model_selector ) == "set":
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143 --theta ${options_type.population_model.T}
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144 --ploidy ${options_type.population_model.P}
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145 ${options_type.population_model.J}
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146 ${options_type.population_model.K}
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147 #end if
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148
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149 ## REFERENCE ALLELE
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150 #if str( $options_type.reference_allele.reference_allele_selector ) == "set":
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151 ${options_type.reference_allele.Z}
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152 --reference-quality '${options_type.reference_allele.reference_quality}'
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153 #end if
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154
6
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155 ## ALLELE SCOPE
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156 #if str( $options_type.allele_scope.allele_scope_selector ) == "set":
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157 ${options_type.allele_scope.I}
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158 ${options_type.allele_scope.i}
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159 ${options_type.allele_scope.X}
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160 ${options_type.allele_scope.u}
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161 ${options_type.allele_scope.no_partial_observations}
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162
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163 -n ${options_type.allele_scope.n}
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164
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165 --haplotype-length ${options_type.allele_scope.haplotype_length}
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166 --min-repeat-size ${options_type.allele_scope.min_repeat_length}
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167 --min-repeat-entropy ${options_type.allele_scope.min_repeat_entropy}
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168 #end if
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169
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170 ## REALIGNMENT
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171 ${options_type.O}
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172
6
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173 ##INPUT FILTERS
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174 #if str( $options_type.input_filters.input_filters_selector ) == "set":
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175 ${options_type.input_filters.use_duplicate_reads}
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176 -m ${options_type.input_filters.m}
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177 -q ${options_type.input_filters.q}
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178 -R ${options_type.input_filters.R}
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179 -Y ${options_type.input_filters.Y}
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180 -e ${options_type.input_filters.e}
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181 -F ${options_type.input_filters.F}
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182 -C ${options_type.input_filters.C}
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183 -G ${options_type.input_filters.G}
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184
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185 #if str( $options_type.input_filters.mismatch_filters.mismatch_filters_selector ) == "set":
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186 -Q ${options_type.input_filters.mismatch_filters.Q}
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187 #if str($options_type.input_filters.mismatch_filters.U)
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188 -U ${options_type.input_filters.mismatch_filters.U}
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189 #end if
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190 -z ${options_type.input_filters.mismatch_filters.z}
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191
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192 --read-snp-limit ${options_type.input_filters.mismatch_filters.read_snp_limit}
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193 #end if
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194
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195 --min-alternate-qsum ${options_type.input_filters.min_alternate_qsum}
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196 #end if
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197
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198 ## POPULATION AND MAPPABILITY PRIORS
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199 #if str( $options_type.population_mappability_priors.population_mappability_priors_selector ) == "set":
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200 ${options_type.population_mappability_priors.k}
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201 ${options_type.population_mappability_priors.w}
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202 ${options_type.population_mappability_priors.V}
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203 ${options_type.population_mappability_priors.a}
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204 #end if
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205
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206 ## GENOTYPE LIKELIHOODS
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207 #if str( $options_type.genotype_likelihoods.genotype_likelihoods_selector ) == "set":
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208 ${$options_type.genotype_likelihoods.experimental_gls}
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209
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210 --base-quality-cap ${$options_type.genotype_likelihoods.base_quality_cap}
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211 --prob-contamination ${$options_type.genotype_likelihoods.prob_contamination}
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212 #end if
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213
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214 ## ALGORITHMIC FEATURES
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215 #if str( $options_type.algorithmic_features.algorithmic_features_selector ) == "set":
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216 -B '${options_type.algorithmic_features.B}'
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217 -W '${options_type.algorithmic_features.W}'
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218 -D '${options_type.algorithmic_features.D}'
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219
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220 #if str($options_type.algorithmic_features.genotype_variant_threshold)
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221 -S ${options_type.algorithmic_features.genotype_variant_threshold}
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222 #end if
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223
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224 ${options_type.algorithmic_features.N}
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225 ${options_type.algorithmic_features.j}
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226 ${options_type.algorithmic_features.H}
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227 ${options_type.algorithmic_features.genotype_qualities}
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228 ${options_type.algorithmic_features.report_genotype_likelihood_max}
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229
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230 --genotyping-max-banddepth ${options_type.algorithmic_features.genotyping_max_banddepth}
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231 #end if
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232 #end if
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233
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234 ";
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235 done > freebayes_commands.sh &&
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236
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237 cat freebayes_commands.sh |
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238 parallel --will-cite -j \${GALAXY_SLOTS:-1} &&
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239
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240 ## make VCF header
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241 grep "^#" "./vcf_output/part_\$i.vcf" > header.txt &&
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242
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243 for i in `cat regions_uniq.bed | awk '{print $1":"$2".."$3}'`;
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244 do
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245 ## if this fails then it bails out the script
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246 cat "./vcf_output/part_\$i.vcf" | grep -v "^#" || true
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247 ;
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248 done | sort -k1,1 -k2,2n -k5,5 -u | cat header.txt - > '${output_vcf}'
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249
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250 #if str( $options_type.options_type_selector ) == "full":
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251 #if str( $options_type.optional_inputs.optional_inputs_selector ) == 'set':
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252 #if $options_type.optional_inputs.output_failed_alleles_option:
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253 &&
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254 for i in `cat regions.bed | awk '{print $1":"$2".."$3}'`;
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255 do
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256 cat "./failed_alleles/part_\$i.bed"
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257 ;
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258 done > '${output_failed_alleles_bed}'
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259 #end if
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260
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261 #if $options_type.optional_inputs.output_trace_option:
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262 &&
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263 for i in `cat regions.bed | awk '{print $1":"$2".."$3}'`;
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264 do
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265 cat './trace/part_\$i.txt'
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266 ;
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267 done > '${output_trace}'
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268 #end if
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269 #end if
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270 #end if
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271 ]]></command>
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272
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273 <inputs>
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274 <conditional name="reference_source">
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275 <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">
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276 <option value="cached">Locally cached</option>
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277 <option value="history">History</option>
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278 </param>
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279 <when value="cached">
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280 <expand macro="input_bam">
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281 <expand macro="validation" />
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282 </expand>
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283 <param name="ref_file" type="select" label="Using reference genome">
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284 <options from_data_table="fasta_indexes" />
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285 <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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286 </param>
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287 </when>
4
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288 <when value="history"> <!-- FIX ME!!!! -->
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289 <expand macro="input_bam" />
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290 <param name="ref_file" type="data" format="fasta" label="Use the following dataset as the reference sequence"
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291 help="You can upload a FASTA sequence to the history and use it as reference" />
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292 </when>
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293 </conditional>
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294 <conditional name="target_limit_type">
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295 <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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296 <option value="do_not_limit" selected="true">Do not limit</option>
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297 <option value="limit_by_target_file">Limit by target file</option>
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298 <option value="limit_by_region">Limit to region</option>
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299 </param>
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300 <when value="do_not_limit" />
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301 <when value="limit_by_target_file">
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302 <param name="input_target_bed" argument="--targets" type="data" format="bed" label="Limit analysis to regions in this BED dataset" />
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303 </when>
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304 <when value="limit_by_region">
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305 <param name="region_chromosome" argument="--region" type="text" label="Region Chromosome" value="" /> <!--only once? -->
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306 <param name="region_start" type="integer" label="Region Start" value="" />
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307 <param name="region_end" type="integer" label="Region End" value="" />
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308 </when>
0
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309 </conditional>
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310 <conditional name="coverage_options">
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311 <param name="coverage_options_selector" type="select" label="Read coverage"
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312 help="Sets --min-coverage, --limit-coverage, and --skip-coverage">
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313 <option value="do_not_set" selected="true">Use defaults</option>
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314 <option value="set">Specify coverage options</option>
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315 </param>
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316 <when value="set">
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317 <expand macro="par_min_cov" />
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318 </when>
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319 <when value="do_not_set" />
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320 </conditional>
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321 <conditional name="options_type">
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322 <param name="options_type_selector" type="select" label="Choose parameter selection level"
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323 help="Select how much control over the freebayes run you need">
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324 <option value="simple" selected="true">1. Simple diploid calling</option>
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325 <option value="simple_w_filters">2. Simple diploid calling with filtering and coverage</option>
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326 <option value="naive">3. Frequency-based pooled calling</option>
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327 <option value="naive_w_filters">4. Frequency-based pooled calling with filtering and coverage</option>
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328 <option value="full">5. Full list of options</option>
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329 </param>
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330 <when value="full">
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331
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332 <conditional name="optional_inputs">
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333 <param name="optional_inputs_selector" type="select" label="Additional inputs"
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334 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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335 <option value="do_not_set" selected="true">Do not provide additional inputs</option>
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336 <option value="set">Provide additional inputs</option>
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337 </param>
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338 <when value="set">
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339 <param name="output_failed_alleles_option" argument="--failed-alleles" type="boolean" truevalue="--failed-alleles" falsevalue="" checked="false"
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340 label="Write out failed alleles file" />
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341 <param name="output_trace_option" argument="--trace" type="boolean" truevalue="--trace" falsevalue="" checked="false"
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342 label="Write out algorithm trace file" />
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343 <param argument="--samples" type="data" format="txt"
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344 label="Limit analysis to samples listed (one per line) in this dataset" optional="true"
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345 help="By default FreeBayes will analyze all samples in its input BAM datasets" />
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346 <param argument="--populations" type="data" format="txt" optional="true"
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347 label="Populations dataset"
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348 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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349 <param name="A" argument="--cnv-map" type="data" format="bed" optional="true"
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350 label="Read a copy number map from a BED dataset"
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351 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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352 <conditional name="input_variant_type">
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353 <param name="input_variant_type_selector" type="select" label="Provide variants dataset">
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354 <option value="do_not_provide" selected="true">Do not provide</option>
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355 <option value="provide_vcf">Provide VCF dataset</option>
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356 </param>
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357 <when value="do_not_provide" />
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358 <when value="provide_vcf">
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359 <param name="input_variant_vcf" argument="--variant-input" type="data" format="vcf_bgzip"
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360 label="Use variants reported in this VCF dataset as input to the algorithm">
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361 <conversion name="Tabixized_input" type="tabix" />
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362 </param>
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363 <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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364 label="Only provide variant calls and genotype likelihoods for sites in VCF" />
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365 </when>
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366 </conditional>
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367 <param name="haplotype_basis_alleles" argument="--haplotype-basis-alleles" type="data" format="vcf" optional="true"
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368 label="Only use variant alleles provided in this input VCF for the construction of complex or haplotype alleles" />
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369 <param name="report_monomorphic" argument="--report-monomorphic" type="boolean" truevalue="--report-monomorphic" falsevalue="" checked="false"
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370 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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371 <param name="observation_bias" argument="--observation-bias" type="data" format="tabular" optional="true"
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372 label="Load read length-dependent allele observation biases from"
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373 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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374 <param name="contamination_estimates" argument="--contamination-estimates" type="data" format="tabular" optional="true"
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375 label="Upload per-sample estimates of contamination from"
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376 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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377 </when>
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378 <when value="do_not_set" />
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379 </conditional>
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380
4
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381 <!-- reporting -->
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382 <conditional name="reporting">
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383 <param name="reporting_selector" type="select" label="Reporting options" help="Sets -P --pvar option">
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384 <option value="do_not_set" selected="true">Use defaults</option>
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385 <option value="set">Set reporting options</option>
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386 </param>
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387 <when value="set">
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388 <param argument="--pvar" type="float" value="0.0"
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389 label="Report sites if the probability that there is a polymorphism at the site is greater than"
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390 help="Note that post-filtering is generally recommended over the use of this parameter" />
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391 </when>
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392 <when value="do_not_set" />
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393 </conditional>
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394
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395 <!-- population model -->
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396 <conditional name="population_model">
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397 <param name="population_model_selector" type="select" label="Population model options"
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398 help="Sets --theta, --ploidy, --pooled-discrete, and --pooled-continuous options">
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399 <option value="do_not_set" selected="true">Use defaults</option>
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400 <option value="set">Set population model options</option>
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401 </param>
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402 <when value="set">
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403 <param name="T" argument="--theta" type="float" value="0.001"
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404 label="The expected mutation rate or pairwise nucleotide diversity among the population under analysis"
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405 help="This serves as the single parameter to the Ewens Sampling Formula prior model" />
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406 <param name="P" argument="--ploidy" type="integer" value="2"
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407 label="Set ploidy for the analysis" />
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408 <param name="J" argument="--pooled-discrete" type="boolean" truevalue="-J" falsevalue="" checked="false"
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409 label="Assume that samples result from pooled sequencing"
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410 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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411 <param name="K" argument="--poled-continuous" type="boolean" truevalue="-K" falsevalue="" checked="false"
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412 label="Output all alleles which pass input filters, regardles of genotyping outcome or model" />
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413 </when>
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414 <when value="do_not_set" />
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415 </conditional>
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416
4
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417 <!-- reference allele -->
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418 <conditional name="reference_allele">
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419 <param name="reference_allele_selector" type="select" label="Reference allele options"
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420 help="Sets --use-reference-allele and --reference-quality options">
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421 <option value="do_not_set" selected="true">Use defaults</option>
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422 <option value="set">Set reference allele options</option>
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423 </param>
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424 <when value="set">
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425 <param name="Z" argument="--use-reference-allele" type="boolean" truevalue="-Z" falsevalue="" checked="false"
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426 label="Include the reference allele in the analysis as if it is another sample from the same population" />
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427 <param name="reference_quality" argument="--reference-quality" type="text" value="100,60"
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428 label="Assign mapping quality of MQ (100) to the reference allele at each site and base quality of BQ (60)" />
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429 </when>
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430 <when value="do_not_set" />
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431 </conditional>
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432
4
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433 <!-- allelic scope -->
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434 <conditional name="allele_scope">
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435 <param name="allele_scope_selector" type="select" label="Allelic scope options"
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diff changeset
436 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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437 <option value="do_not_set" selected="true">Use defaults</option>
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438 <option value="set">Set alleic scope options</option>
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diff changeset
439 </param>
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440 <when value="set">
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parents: 8
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441 <param name="I" argument="--no-snps" type="boolean" truevalue="-I" falsevalue="" checked="false"
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parents: 8
diff changeset
442 label="Ignore SNP alleles" />
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parents: 8
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443 <param name="i" argument="--no-indels" type="boolean" truevalue="-i" falsevalue="" checked="false"
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parents: 8
diff changeset
444 label="Ignore indels alleles" />
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parents: 8
diff changeset
445 <param name="X" argument="--no-mnps" type="boolean" truevalue="-X" falsevalue="" checked="false"
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parents: 8
diff changeset
446 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
447 <param name="u" argument="--no-complex" type="boolean" truevalue="-u" falsevalue="" checked="false"
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parents: 8
diff changeset
448 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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449 <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
450 label="How many best SNP alleles to evaluate"
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parents: 8
diff changeset
451 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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452 <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
453 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
454 <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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455 label="When assembling observations across repeats, require the total repeat length at least this many bp" />
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parents: 10
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456 <param name="min_repeat_entropy" argument="--min-repeat-entropy" type="integer" value="1"
9
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parents: 8
diff changeset
457 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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458 <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
459 label="Exclude observations which do not fully span the dynamically-determined detection window"
9
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parents: 8
diff changeset
460 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
461 </when>
9
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parents: 8
diff changeset
462 <when value="do_not_set" />
4
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parents: 3
diff changeset
463 </conditional>
6
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parents: 5
diff changeset
464
4
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parents: 3
diff changeset
465 <!-- indel realignment -->
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parents: 8
diff changeset
466 <param name="O" argument="--dont-left-align-indels" type="boolean" truevalue="-O" falsevalue="" checked="false"
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parents: 8
diff changeset
467 label="Turn off left-alignment of indels" />
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parents: 5
diff changeset
468
4
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parents: 3
diff changeset
469 <!-- input filters -->
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parents: 3
diff changeset
470 <conditional name="input_filters">
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parents: 3
diff changeset
471 <param name="input_filters_selector" type="select" label="Input filters"
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parents: 8
diff changeset
472 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
473 <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
474 <option value="set">Set input filters</option>
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parents: 3
diff changeset
475 </param>
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parents: 5
diff changeset
476 <when value="set">
9
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parents: 8
diff changeset
477 <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
478 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
479 <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
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parents: 8
diff changeset
480 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
481 <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
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parents: 8
diff changeset
482 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
483 <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
iuc
parents: 8
diff changeset
484 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
485 <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
486 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
487 <conditional name="mismatch_filters">
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diff changeset
488 <param name="mismatch_filters_selector" type="select" label="Mismatch filters"
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parents: 5
diff changeset
489 help="Sets -Q, -U, -z, and &#36; options">
4
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diff changeset
490 <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
diff changeset
491 <option value="set">Set mismatch filters</option>
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parents: 3
diff changeset
492 </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
493 <when value="set">
9
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parents: 8
diff changeset
494 <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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diff changeset
495 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
496 <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
497 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
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parents: 8
diff changeset
498 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
499 <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
500 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
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parents: 8
diff changeset
501 <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
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parents: 8
diff changeset
502 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
503 help="default=~unbounded" />
4
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parents: 3
diff changeset
504 </when>
9
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parents: 8
diff changeset
505 <when value="do_not_set" />
4
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diff changeset
506 </conditional>
9
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parents: 8
diff changeset
507 <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
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parents: 8
diff changeset
508 label="Exclude reads with more than this number of separate gaps"
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iuc
parents: 8
diff changeset
509 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
510 <param name="standard_filters" argument="--standard-filters" type="boolean" truevalue="-0" falsevalue="" checked="false"
6
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parents: 5
diff changeset
511 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
512 help="Equivalent to -m 30 -q 20 -R 0 -S 0" />
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parents: 10
diff changeset
513 <param name="F" argument="--min-alternate-fraction" type="float" value="0.05"
9
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parents: 8
diff changeset
514 label="Require at least this fraction of observations supporting an alternate allele within a single individual in the in order to evaluate the position" />
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 <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
516 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
517 <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
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parents: 8
diff changeset
518 label="Require at least this sum of quality of observations supporting an alternate allele within a single individual in order to evaluate the position" />
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parents: 8
diff changeset
519 <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
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parents: 8
diff changeset
520 label="Require at least this count of observations supporting an alternate allele within the total population in order to use the allele in analysis" />
4
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diff changeset
521 </when>
9
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parents: 8
diff changeset
522 <when value="do_not_set" />
4
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parents: 3
diff changeset
523 </conditional>
6
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parents: 5
diff changeset
524
4
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parents: 3
diff changeset
525 <!-- population and mappability priors -->
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parents: 3
diff changeset
526 <conditional name="population_mappability_priors">
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parents: 3
diff changeset
527 <param name="population_mappability_priors_selector" type="select" label="Population and mappability priors"
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parents: 8
diff changeset
528 help="Sets -k, -w, -V, and -a options">
4
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parents: 3
diff changeset
529 <option value="do_not_set" selected="true">Use defaults</option>
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parents: 3
diff changeset
530 <option value="set">Set population and mappability priors</option>
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parents: 3
diff changeset
531 </param>
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parents: 3
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532 <when value="set">
9
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parents: 8
diff changeset
533 <param name="k" argument="--no-population-priors" type="boolean" truevalue="-k" falsevalue="" checked="false"
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parents: 8
diff changeset
534 label="No population priors"
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parents: 8
diff changeset
535 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
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parents: 8
diff changeset
536 <param name="w" argument="--hwe-priors-off" type="boolean" truevalue="-w" falsevalue="" checked="false"
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parents: 8
diff changeset
537 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
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parents: 8
diff changeset
538 <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
539 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
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parents: 8
diff changeset
540 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
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parents: 8
diff changeset
541 <param name="a" argument="--allele-balance-priors-off" type="boolean" truevalue="-a" falsevalue="" checked="false"
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parents: 8
diff changeset
542 label="Disable use of aggregate probability of observation balance between alleles as a component of the priors" />
4
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diff changeset
543 </when>
9
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parents: 8
diff changeset
544 <when value="do_not_set" />
4
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diff changeset
545 </conditional>
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parents: 5
diff changeset
546
4
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parents: 3
diff changeset
547 <!-- genotype likelihoods -->
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parents: 3
diff changeset
548 <conditional name="genotype_likelihoods">
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parents: 3
diff changeset
549 <param name="genotype_likelihoods_selector" type="select" label="Genotype likelihood options"
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parents: 8
diff changeset
550 help="Sets --base-quality-cap, --experimental-gls, and --prob-contamination options">
4
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parents: 3
diff changeset
551 <option value="do_not_set" selected="true">Use defaults</option>
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parents: 3
diff changeset
552 <option value="set">Set genotype likelihood options</option>
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parents: 3
diff changeset
553 </param>
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parents: 3
diff changeset
554 <when value="set">
9
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iuc
parents: 8
diff changeset
555 <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
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parents: 8
diff changeset
556 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
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parents: 8
diff changeset
557 <param name="experimental_gls" argument="--experimental-gls" type="boolean" truevalue="--experimental-gls" falsevalue="" checked="false"
6
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parents: 5
diff changeset
558 label="Generate genotype likelihoods using 'effective base depth' metric qual = 1-BaseQual * 1-MapQual"
9
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parents: 8
diff changeset
559 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
560 <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
561 label="An estimate of contamination to use for all samples" />
4
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parents: 3
diff changeset
562 </when>
9
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parents: 8
diff changeset
563 <when value="do_not_set" />
4
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parents: 3
diff changeset
564 </conditional>
6
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iuc
parents: 5
diff changeset
565
4
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parents: 3
diff changeset
566 <!-- algorithmic features -->
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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parents: 3
diff changeset
567 <conditional name="algorithmic_features">
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parents: 3
diff changeset
568 <param name="algorithmic_features_selector" type="select" label="Algorithmic features"
6
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iuc
parents: 5
diff changeset
569 help="Sets --report-genotypes-likelihood-max, -B, --genotyping-max-banddepth, -W, -N, S, -j, -H, -D, -= options">
4
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parents: 3
diff changeset
570 <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
571 <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
572 </param>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
573 <when value="set">
9
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iuc
parents: 8
diff changeset
574 <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
575 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
576 <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
577 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
578 <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
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parents: 8
diff changeset
579 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
580 <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
581 label="Integrate all genotype combinations in our posterior space which include no more than N (1) samples with their Mth (3) best data likelihood" />
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
582 <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
583 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
584 <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
585 label="Limit posterior integration to samples where the second-best genotype likelihood is no more than log(N) from the highest genotype likelihood for the sample"
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
586 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
587 <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
588 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
589 <param name="H" argument="--harmonic-indel-quality" type="boolean" truevalue="-H" falsevalue="" checked="false"
6
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parents: 5
diff changeset
590 label="Use a weighted sum of base qualities around an indel, scaled by the distance from the indel"
9
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iuc
parents: 8
diff changeset
591 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
592 <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
593 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
594 <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
595 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
596 </when>
9
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iuc
parents: 8
diff changeset
597 <when value="do_not_set" />
4
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parents: 3
diff changeset
598 </conditional>
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
599 </when>
9
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parents: 8
diff changeset
600 <when value="simple" />
11
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
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parents: 10
diff changeset
601 <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
602 <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
603 <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
604 </conditional>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
605 </inputs>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
606 <outputs>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
607 <data format="vcf" name="output_vcf" label="${tool.name} on ${on_string} (variants)" />
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
608 <data format="bed" name="output_failed_alleles_bed" label="${tool.name} on ${on_string} (failed alleles)">
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
609 <filter>( options_type['options_type_selector'] == 'cline' or options_type['options_type_selector'] == 'full' ) and options_type['optional_inputs']['optional_inputs_selector'] == 'set' and options_type['optional_inputs']['output_failed_alleles_option'] is True</filter>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
610 </data>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
611 <data format="txt" name="output_trace" label="${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
612 <filter>( options_type['options_type_selector'] == 'cline' or options_type['options_type_selector'] == 'full' ) and options_type['optional_inputs']['optional_inputs_selector'] == 'set' and options_type['optional_inputs']['output_trace_option'] is True</filter>
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 </outputs>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
615 <tests>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
616 <test>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
617 <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
618 <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
619 <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
620 <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
621 <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
622 <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
623 </test>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
624 <test>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
625 <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
626 <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
627 <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
628 <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
629 <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
630 <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
631 <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
632 <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
633 </test>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
634 <test>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
635 <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
636 <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
637 <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
638 <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
639 <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
640 <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
641 <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
642 <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
643 </test>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
644 <test>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
645 <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
646 <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
647 <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
648 <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
649 <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
650 <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
651 <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
652 <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
653 </test>
11
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
654 <test>
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
655 <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
656 <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
657 <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
658 <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
659 <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
660 <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
661 <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
662 <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
663 </test>
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
664 <test>
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
665 <param name="reference_source_selector" value="history" />
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
666 <param name="processmode" value="individual" />
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
667 <param name="ref_file" ftype="fasta" value="freebayes-hxb2.fasta"/>
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
668 <param name="input_bams" ftype="bam" value="freebayes-hxb2.bam"/>
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
669 <param name="options_type_selector" value="simple"/>
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
670 <param name="coverage_options_selector" value="set" />
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
671 <param name="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
672 <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
673 </test>
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
674 <test>
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
675 <param name="reference_source_selector" value="history" />
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
676 <param name="processmode" value="individual" />
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
677 <param name="ref_file" ftype="fasta" value="freebayes-hxb2.fasta"/>
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
678 <param name="input_bams" ftype="bam" value="freebayes-hxb2.bam"/>
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
679 <param name="options_type_selector" value="simple"/>
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
680 <param name="coverage_options_selector" value="set" />
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
681 <param name="skip_coverage" value="100" />
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
682 <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"
iuc
parents: 10
diff changeset
683 </test>
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
684 </tests>
11
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685 <help><![CDATA[
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686 **What it does**
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687
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688 FreeBayes is a Bayesian genetic variant detector designed to find small polymorphisms, specifically SNPs (single-nucleotide polymorphisms), indels (insertions and deletions), MNPs (multi-nucleotide polymorphisms), and complex events (composite insertion and substitution events) smaller than the length of a short-read sequencing alignment.
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689
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690 See https://github.com/ekg/freebayes for details on FreeBayes.
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691
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692 ------
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693
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694 **Description**
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695
9
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
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696 Provided some BAM dataset(s) and a reference sequence, FreeBayes will produce a VCF dataset describing SNPs, indels, and complex variants in samples in the input alignments.
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697
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698 By default, FreeBayes will consider variants supported by at least 2 observations in a single sample (-C) and also by at least 20% of the reads from a single sample (-F). These settings are suitable to low to high depth sequencing in haploid and diploid samples, but users working with polyploid or pooled samples may wish to adjust them depending on the characteristics of their sequencing data.
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699
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700 FreeBayes is capable of calling variant haplotypes shorter than a read length where multiple polymorphisms segregate on the same read. The maximum distance between polymorphisms phased in this way is determined by the --max-complex-gap, which defaults to 3bp. In practice, this can comfortably be set to half the read length.
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701
2
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702 Ploidy may be set to any level (-p), but by default all samples are assumed to be diploid. FreeBayes can model per-sample and per-region variation in copy-number (-A) using a copy-number variation map.
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703
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704 FreeBayes can act as a frequency-based pooled caller and describe variants and haplotypes in terms of observation frequency rather than called genotypes. To do so, use --pooled-continuous and set input filters to a suitable level. Allele observation counts will be described by AO and RO fields in the VCF output.
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705
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706 -------
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707
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708 **Galaxy-specific options**
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709
9
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
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710 Galaxy allows five levels of control over FreeBayes options, provided by the **Choose parameter selection level** menu option. These are:
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711
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c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
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712 1. *Simple diploid calling*: The simplest possible FreeBayes application. Equivalent to using FreeBayes with only a BAM input and no other parameter options.
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
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713 2. *Simple diploid calling with filtering and coverage*: Same as #1 plus two additional options: -0 (standard filters: --min-mapping-quality 30 --min-base-quality 20 --min-supporting-allele-qsum 0 --genotype-variant-threshold 0) and --min-coverage.
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
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714 3. *Frequency-based pooled calling*: This is equivalent to using FreeBayes with the following options: --haplotype-length 0 --min-alternate-count 1 --min-alternate-fraction 0 --pooled-continuous --report-monomorphic. This is the best choice for calling variants in mixtures such as viral, bacterial, or organellar genomes.
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
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715 4. *Frequency-based pooled calling with filtering and coverage*: Same as #3 but adds -0 and --min-coverage like in #2.
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
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716 5. *Complete list of all options*: Gives you full control by exposing all FreeBayes options as Galaxy parameters.
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717
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718 ------
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719
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720 **Command-line parameters**
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721
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
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722 **Input**::
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
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723
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724 --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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725 --bam-list FILE A file containing a list of BAM files to be analyzed.
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726
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
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727 --stdin Read BAM input on stdin.
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728 --fasta-reference FILE Use FILE as the reference sequence for analysis.
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
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729 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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730 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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731 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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732 --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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733 --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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734 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
735 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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736 --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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737 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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738 BAM files.
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
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739 --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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740 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
741 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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742 --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
743 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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744 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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745 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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746 seq_name start end sample_name copy_number
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747 ... for each region in each sample which does not have the
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
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748 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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749 by space or tab.
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750
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751 **Output**::
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
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752
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
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753 --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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754 --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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755 --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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756 --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
757 set to "true" , will also route an int to --gvcf-chunk
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
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parents: 10
diff changeset
758 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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759 --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
760 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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761 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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762 --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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763 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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764 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
765 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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766 --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
767 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
768 alleles.
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
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diff changeset
769 --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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770 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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771 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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772 --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
773 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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774 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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775 --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"
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776 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"
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diff changeset
777 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"
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778 --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"
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779
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
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780 **Population model**::
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
781
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
782 --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
783 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
784 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
785 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
786 --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
787 --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
788 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
789 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
790 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
791 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
792 --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
793 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
794
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
795 **Reference allele**::
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
796
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
797 --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
798 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
799 --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
800 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
801
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
802 **Allele scope**::
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
803
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
804 --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
805 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
806 --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
807 --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
808 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
809 --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
810 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
811 --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
812 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
813 --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
814 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
815 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
816
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
817 **Indel realignment**::
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
818
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
819 --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
820
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
821 **Input filters**::
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
822
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
823 --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
824 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
825 --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
826 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
827 --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
828 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
829 --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
830 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
831 --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
832 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
833 --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
834 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
835 --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
836 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
837 default: ~unbounded
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
838 --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
839 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
840 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
841 --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
842 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
843 default: ~unbounded
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
844 --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
845 default: ~unbounded
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
846 --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
847 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
848 --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
849 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
850 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
851 --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
852 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
853 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
854 --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
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: 0
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-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
858 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
859 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
860 --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
861 --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
862 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
863 --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
864 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
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
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
867 **Population priors**::
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
868
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
869 --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
870 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
871
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
872 **Mappability priors**::
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
873
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
874 --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
875 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
876 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
877 --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
878 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
879 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
880 --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
881 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
882
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
883 **Genotype likelihoods**::
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
884
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
885 --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
886 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
887 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
888 --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
889 --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
890 --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
891 --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
892 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
893 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
894 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
895
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
896 **Algorithmic features**::
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
897
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
898 --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
899 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
900 --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
901 --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
902 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
903 --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
904 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
905 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
906 --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
907 --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
908 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
909 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
910 --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
911 --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
912 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
913 --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
914 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
915 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
916 --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
917 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
918
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
919 ------
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
920
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
921 **Acknowledgments**
0
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
922
2
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
923 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
924 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
925 ]]>
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
926 </help>
10
2fb16f415220 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 99e8a87a2993ae644df15756044a40a42aa7a05b
iuc
parents: 9
diff changeset
927 <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
928 <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
929 @article{Tange2011a,
2fb16f415220 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 99e8a87a2993ae644df15756044a40a42aa7a05b
iuc
parents: 9
diff changeset
930 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
931 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
932 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
933 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
934 month = {Feb},
2fb16f415220 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 99e8a87a2993ae644df15756044a40a42aa7a05b
iuc
parents: 9
diff changeset
935 number = {1},
2fb16f415220 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 99e8a87a2993ae644df15756044a40a42aa7a05b
iuc
parents: 9
diff changeset
936 volume = {36},
2fb16f415220 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 99e8a87a2993ae644df15756044a40a42aa7a05b
iuc
parents: 9
diff changeset
937 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
938 year = {2011},
2fb16f415220 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 99e8a87a2993ae644df15756044a40a42aa7a05b
iuc
parents: 9
diff changeset
939 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
940 }
2fb16f415220 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 99e8a87a2993ae644df15756044a40a42aa7a05b
iuc
parents: 9
diff changeset
941 </citation>
2fb16f415220 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 99e8a87a2993ae644df15756044a40a42aa7a05b
iuc
parents: 9
diff changeset
942 </expand>
0
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
943 </tool>