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annotate freebayes.xml @ 23:52aed7d9ed2b draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
author devteam
date Sun, 25 Sep 2016 09:48:24 -0400
parents 99684adf84de
children da6e10dee68b
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1 <tool id="freebayes" name="FreeBayes" version="1.0.2.29--1">
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2 <description> - bayesian genetic variant detector</description>
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3 <requirements>
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4 <requirement type="package" version="1.0.2.29">freebayes</requirement>
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5 <requirement type="package" version="0.1.19">samtools</requirement>
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6 <requirement type="package" version="4.1.3">gawk</requirement>
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7 <requirement type="package" version="20160622">parallel</requirement>
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8 </requirements>
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9 <stdio>
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10 <exit_code range="1:" />
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11 </stdio>
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12 <command>
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13 <![CDATA[
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14 ##set up input files
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15
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16 #set $reference_fasta_filename = "localref.fa"
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17
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18 #if str( $reference_source.reference_source_selector ) == "history":
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19 ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &&
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20 samtools faidx "${reference_fasta_filename}" 2>&1 || echo "Error running samtools faidx for FreeBayes" >&2 &&
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21 #else:
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22 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
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23 #end if
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24
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25 #for $bam_count, $input_bam in enumerate( $reference_source.input_bams ):
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26 ln -s "${input_bam}" "b_${bam_count}.bam" &&
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27 ln -s "${input_bam.metadata.bam_index}" "b_${bam_count}.bam.bai" &&
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28 #end for
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29
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30 ## Tabixize optional input_varinat_vcf file (for --variant-input option)
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31 #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( $options_type.optional_inputs.input_variant_type.input_variant_type_selector ) == "provide_vcf":
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32 ln -s "${options_type.optional_inputs.input_variant_type.input_variant_vcf}" "input_variant_vcf.vcf.gz" &&
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33 ln -s "${Tabixized_input}" "input_variant_vcf.vcf.gz.tbi" &&
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34 #end if
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35
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36 #for $bam_count, $input_bam in enumerate( $reference_source.input_bams ):
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37 samtools view -H b_${bam_count}.bam | grep "^@SQ" | cut -f 2- | awk '{ gsub("^SN:","",$1); gsub("^LN:","",$2); print $1"\t0\t"$2; }' >> regions_all.bed &&
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38 #end for
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40 sort -u regions_all.bed > regions_uniq.bed &&
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41 ## split into even small chunks, this has some disatvantages and will not be used for the moment
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42 ## bedtools makewindows -b regions_uniq.bed -w 10000000 -s 9990000 > regions.bed &&
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44 mkdir vcf_output &&
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45 mkdir failed_alleles &&
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46 mkdir trace &&
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48 ## Finished setting up inputs
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50 for i in `cat regions_uniq.bed | awk '{print $1":"$2".."$3}'`;
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51 do
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53 echo "
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55 ## COMMAND LINE STARTS HERE
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57 freebayes
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59 --region '\$i'
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61 #for $bam_count, $input_bam in enumerate( $reference_source.input_bams ):
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62 --bam 'b_${bam_count}.bam'
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63 #end for
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64 --fasta-reference '${reference_fasta_filename}'
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65
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66 ## Outputs
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67 --vcf './vcf_output/part_\$i.vcf'
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68
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69 #if str( $target_limit_type.target_limit_type_selector ) == "limit_by_target_file":
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70 --targets '${target_limit_type.input_target_bed}'
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71 #elif str( $target_limit_type.target_limit_type_selector ) == "limit_by_region":
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72 --region '${target_limit_type.region_chromosome}:${target_limit_type.region_start}..${target_limit_type.region_end}'
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73 #end if
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74
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75 ##advanced options
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76 #if str( $options_type.options_type_selector ) == "simple":
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77 ##do nothing as command like build up to this point is sufficinet for simple diploid calling
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78
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79 #elif str( $options_type.options_type_selector ) == "simple_w_filters":
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80 --standard-filters
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81 --min-coverage '${options_type.min_coverage}'
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82 #elif str( $options_type.options_type_selector ) == "naive":
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83 --haplotype-length 0
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84 --min-alternate-count 1
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85 --min-alternate-fraction 0
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86 --pooled-continuous
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87 --report-monomorphic
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88 #elif str( $options_type.options_type_selector ) == "naive_w_filters":
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89 --haplotype-length 0
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90 --min-alternate-count 1
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91 --min-alternate-fraction 0
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92 --pooled-continuous
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93 --report-monomorphic
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94 --standard-filters
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95 --min-coverage '${options_type.min_coverage}'
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96
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97 ## Command line direct text entry is not allowed at this time for security reasons
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98 #elif str( $options_type.options_type_selector ) == "full":
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99 #if str( $options_type.optional_inputs.optional_inputs_selector ) == 'set':
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100 ${options_type.optional_inputs.report_monomorphic}
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101
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102 #if $options_type.optional_inputs.output_trace_option:
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103 --trace ./trace/part_'\$i'.txt
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104 #end if
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105 #if $options_type.optional_inputs.output_failed_alleles_option:
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106 --failed-alleles ./failed_alleles/part_'\$i'.bed
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107 #end if
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108 #if $options_type.optional_inputs.samples:
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109 --samples '${options_type.optional_inputs.samples}'
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110 #end if
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111 #if $options_type.optional_inputs.populations:
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112 --populations '${options_type.optional_inputs.populations}'
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113 #end if
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114 #if $options_type.optional_inputs.A:
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115 --cnv-map '${options_type.optional_inputs.A}'
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116 #end if
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117 #if str( $options_type.optional_inputs.input_variant_type.input_variant_type_selector ) == "provide_vcf":
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118 --variant-input 'input_variant_vcf.vcf.gz' ## input_variant_vcf.vcf.gz is symlinked to a galaxy-generated dataset in "Tabixize optional input_varinat_vcf file" section of the command line above
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119 ${options_type.optional_inputs.input_variant_type.only_use_input_alleles}
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120 #end if
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121 #if $options_type.optional_inputs.haplotype_basis_alleles:
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122 --haplotype-basis-alleles '${options_type.optional_inputs.haplotype_basis_alleles}'
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123 #end if
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124 #if $options_type.optional_inputs.observation_bias:
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125 --observation-bias '${options_type.optional_inputs.observation_bias}'
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126 #end if
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127 #if $options_type.optional_inputs.contamination_estimates:
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128 --contamination-estimates '${options_type.optional_inputs.contamination_estimates}'
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129 #end if
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130 #end if
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131
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132 ## REPORTING
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133 #if str( $options_type.reporting.reporting_selector ) == "set":
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134 --pvar ${options_type.reporting.pvar}
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135 #end if
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136 ## POPULATION MODEL
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137 #if str( $options_type.population_model.population_model_selector ) == "set":
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138 --theta '${options_type.population_model.T}'
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139 --ploidy '${options_type.population_model.P}'
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140 ${options_type.population_model.J}
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141 ${options_type.population_model.K}
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142 #end if
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143
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144 ## REFERENCE ALLELE
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145 #if str( $options_type.reference_allele.reference_allele_selector ) == "set":
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146 ${options_type.reference_allele.Z}
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147 --reference-quality '${options_type.reference_allele.reference_quality}'
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148 #end if
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149
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150 ## ALLELE SCOPE
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151 #if str( $options_type.allele_scope.allele_scope_selector ) == "set":
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152 ${options_type.allele_scope.I}
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153 ${options_type.allele_scope.i}
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154 ${options_type.allele_scope.X}
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155 ${options_type.allele_scope.u}
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156 -n '${options_type.allele_scope.n}'
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157 --haplotype-length '${options_type.allele_scope.haplotype_length}'
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158 --min-repeat-size '${options_type.allele_scope.min_repeat_length}'
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159 --min-repeat-entropy '${options_type.allele_scope.min_repeat_entropy}'
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160 ${options_type.allele_scope.no_partial_observations}
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161 #end if
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162
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163 ## REALIGNMENT
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164 ${options_type.O}
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165
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166 ##INPUT FILTERS
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167 #if str( $options_type.input_filters.input_filters_selector ) == "set":
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168 ${options_type.input_filters.use_duplicate_reads}
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169 -m '${options_type.input_filters.m}'
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170 -q '${options_type.input_filters.q}'
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171 -R '${options_type.input_filters.R}'
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172 -Y '${options_type.input_filters.Y}'
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173
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174 #if str( $options_type.input_filters.mismatch_filters.mismatch_filters_selector ) == "set":
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175 -Q '${options_type.input_filters.mismatch_filters.Q}'
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176 -U '${options_type.input_filters.mismatch_filters.U}'
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177 -z '${options_type.input_filters.mismatch_filters.z}'
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178 --read-snp-limit '${options_type.input_filters.mismatch_filters.read_snp_limit}'
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179 #end if
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180
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181 -e '${options_type.input_filters.e}'
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182 -F '${options_type.input_filters.F}'
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183 -C '${options_type.input_filters.C}'
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184 --min-alternate-qsum "${options_type.input_filters.min_alternate_qsum}"
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185 -G '${options_type.input_filters.G}'
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186 --min-coverage '${options_type.input_filters.min_coverage}'
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187 #end if
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188
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189 ## POPULATION AND MAPPABILITY PRIORS
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190 #if str( $options_type.population_mappability_priors.population_mappability_priors_selector ) == "set":
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191 ${options_type.population_mappability_priors.k}
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192 ${options_type.population_mappability_priors.w}
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193 ${options_type.population_mappability_priors.V}
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194 ${options_type.population_mappability_priors.a}
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195 #end if
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196
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197 ## GENOTYPE LIKELIHOODS
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198 #if str( $options_type.genotype_likelihoods.genotype_likelihoods_selector ) == "set":
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199 --base-quality-cap '${$options_type.genotype_likelihoods.base_quality_cap}'
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200 ${$options_type.genotype_likelihoods.experimental_gls}
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201 --prob-contamination '${$options_type.genotype_likelihoods.prob_contamination}'
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202 #end if
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203
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204 ## ALGORITHMIC FEATURES
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205 #if str( $options_type.algorithmic_features.algorithmic_features_selector ) == "set":
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206 ${options_type.algorithmic_features.report_genotype_likelihood_max}
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207 -B '${options_type.algorithmic_features.B}'
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208 --genotyping-max-banddepth '${options_type.algorithmic_features.genotyping_max_banddepth}'
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209 -W '${options_type.algorithmic_features.W}'
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210 ${options_type.algorithmic_features.N}
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211
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212 #if str( $options_type.algorithmic_features.genotype_variant_threshold.genotype_variant_threshold_selector ) == "set":
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213 -S '${options_type.algorithmic_features.genotype_variant_threshold.S}'
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214 #end if
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215
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216 ${options_type.algorithmic_features.j}
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217 ${options_type.algorithmic_features.H}
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218 -D '${options_type.algorithmic_features.D}'
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219 ${options_type.algorithmic_features.genotype_qualities}
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220 #end if
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221 #end if
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222
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223 ";
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224 done > freebayes_commands.sh &&
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225 cat freebayes_commands.sh | parallel --no-notice -j \${GALAXY_SLOTS:-1} &&
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226
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227 ## make VCF header
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228
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229 grep "^#" "./vcf_output/part_\$i.vcf" > header.txt &&
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230
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231 for i in `cat regions_uniq.bed | awk '{print $1":"$2".."$3}'`;
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232 do
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233 ## if this fails then it bails out the script
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234 cat "./vcf_output/part_\$i.vcf" | grep -v "^#" || true
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235 ;
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236 done | sort -k1,1 -k2,2n -k5,5 -u | cat header.txt - > "${output_vcf}"
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237
23
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238 #if str( $options_type.options_type_selector ) == "full":
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239 #if str( $options_type.optional_inputs.optional_inputs_selector ) == 'set':
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240 #if $options_type.optional_inputs.output_failed_alleles_option:
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241 &&
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242 for i in `cat regions.bed | awk '{print $1":"$2".."$3}'`;
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243 do
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244 cat "./failed_alleles/part_\$i.bed"
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245 ;
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246 done > '${output_failed_alleles_bed}'
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247 #end if
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248
23
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249 #if $options_type.optional_inputs.output_trace_option:
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250 &&
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251 for i in `cat regions.bed | awk '{print $1":"$2".."$3}'`;
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252 do
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253 cat './trace/part_\$i.txt'
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254 ;
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255 done > '${output_trace}'
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256 #end if
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257 #end if
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258 #end if
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259 ]]>
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260 </command>
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261
23
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262 <inputs>
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263 <conditional name="reference_source">
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264 <param name="reference_source_selector" type="select" label="Load reference genome from">
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265 <option value="cached">Local cache</option>
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266 <option value="history">History</option>
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267 </param>
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268 <when value="cached">
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269 <param name="input_bams" type="data" format="bam" multiple="True" label="BAM file">
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270 <validator type="unspecified_build" />
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271 <validator type="dataset_metadata_in_data_table" table_name="fasta_indexes" metadata_name="dbkey" metadata_column="1" message="Sequences are not currently available for the specified build." />
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272 </param>
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273 <param name="ref_file" type="select" label="Using reference genome">
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274 <options from_data_table="fasta_indexes"></options>
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275 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
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276 </param>
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277 </when>
23
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278 <when value="history"> <!-- FIX ME!!!! -->
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279 <param name="input_bams" type="data" format="bam" multiple="True" label="BAM file" />
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280 <param name="ref_file" type="data" format="fasta" label="Use the following dataset as the reference sequence"
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281 help="You can upload a FASTA sequence to the history and use it as reference" />
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282 </when>
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283 </conditional>
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284 <conditional name="target_limit_type">
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285 <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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286 <option value="do_not_limit" selected="True">Do not limit</option>
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287 <option value="limit_by_target_file">Limit by target file</option>
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288 <option value="limit_by_region">Limit to region</option>
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289 </param>
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290 <when value="do_not_limit">
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291 <!-- Do nothing here -->
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292 </when>
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293 <when value="limit_by_target_file">
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294 <param name="input_target_bed" type="data" format="bed" label="Limit analysis to targets listed in the BED-format FILE." help="-t --targets"/>
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295 </when>
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296 <when value="limit_by_region">
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297 <param name="region_chromosome" type="text" label="Region Chromosome" value="" help="-r --region"/> <!--only once? -->
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298 <param name="region_start" type="integer" label="Region Start" value="" />
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299 <param name="region_end" type="integer" label="Region End" value="" />
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300 </when>
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301 </conditional>
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302 <conditional name="options_type">
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303 <param name="options_type_selector" type="select" label="Choose parameter selection level" help="Select how much control over the freebayes run you need" >
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304 <option value="simple" selected="True">1:Simple diploid calling</option>
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305 <option value="simple_w_filters">2:Simple diploid calling with filtering and coverage</option>
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306 <option value="naive">3:Frequency-based pooled calling</option>
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307 <option value="naive_w_filters">4:Frequency-based pooled calling with filtering and coverage</option>
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308 <option value="full">5:Complete list of all options</option>
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309 <!-- We will not alloow command line text boxes at this time
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310 <option value="cline">6:Input parameters on the command line</option>
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311 -->
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312 </param>
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313 <when value="full">
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314 <conditional name="optional_inputs">
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315 <param name="optional_inputs_selector" type="select" label="Additional inputs"
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316 help="Sets --samples, --populations, --cnv-map, --trace, --failed-alleles, --varinat-input, --only-use-input-alleles, --haplotype-basis-alleles,
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317 --report-all-haplotype-alleles, --report-monomorphic options, --observation-bias, and --contamination-estimates">
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318 <option value="do_not_set" selected="true">Do not provide additional inputs</option>
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319 <option value="set">Provide additional inputs</option>
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320 </param>
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321 <when value="set">
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322 <param name="output_failed_alleles_option" type="boolean" truevalue="--failed-alleles" falsevalue="" checked="False"
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323 label="Write out failed alleles file" help="--failed-alleles" />
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324 <param name="output_trace_option" type="boolean" truevalue="--trace" falsevalue="" checked="False"
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325 label="Write out algorithm trace file" help="--trace"/>
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326 <param name="samples" type="data" format="txt" label="Limit analysis to samples listed (one per line) in the FILE" optional="True"
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327 help="-s --samples; default=By default FreeBayes will analyze all samples in its input BAM files"/>
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328 <param name="populations" type="data" format="txt" label="Populations File" optional="True"
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329 help="--populations; default=False. Each line of FILE should list a sample and a population which it is part of.
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330 The population-based bayesian inference model will then be partitioned on the basis of the populations" />
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331 <param name="A" type="data" format="bed" label="Read a copy number map from the BED file FILE" optional="True"
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332 help="-A --cnv-map; default=copy number is set to as specified by --ploidy. Read a copy number map from the BED file FILE, which has the format:
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333 reference sequence, start, end, sample name, copy number ... for each region in each sample which does not have the default copy number as set by --ploidy."/>
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334 <conditional name="input_variant_type">
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335 <param name="input_variant_type_selector" type="select" label="Provide variants file">
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336 <option value="do_not_provide" selected="True">Do not provide</option>
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337 <option value="provide_vcf">Provide VCF file</option>
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338 </param>
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339 <when value="do_not_provide">
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340 <!-- Do nothing here -->
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341 </when>
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342 <when value="provide_vcf">
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343 <param name="input_variant_vcf" type="data" format="vcf_bgzip" label="Use variants reported in VCF file as input to the algorithm">
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344 <conversion name="Tabixized_input" type="tabix" />
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345 </param>
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346 <param name="only_use_input_alleles" type="boolean" truevalue="--only-use-input-alleles" falsevalue="" checked="False" label="Only provide variant calls and genotype likelihoods for sites in VCF" />
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347 </when>
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348 </conditional>
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349 <param name="haplotype_basis_alleles" type="data" format="vcf" label="Only use variant alleles provided in this input VCF for the construction of complex or haplotype alleles" optional="True"
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350 help="--haplotype-basis-alleles" />
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351 <param name="report_monomorphic" type="boolean" truevalue="--report-monomorphic" falsevalue="" checked="False"
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352 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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353 help="--report-monomorphic " />
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354 <param name="observation_bias" optional="True" type="data" format="tabular" label="Load read length-dependent allele observation biases from"
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355 help="--observation-bias; 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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356 <param name="contamination_estimates" optional="True" type="data" format="tabular" label="Upload per-sample estimates of contamination from"
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357 help="--contamination-estimates; 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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358 </when>
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359 <when value="do_not_set">
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360 <!-- do nothing -->
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361 </when>
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362 </conditional>
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363 <!-- reporting -->
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364 <conditional name="reporting">
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365 <param name="reporting_selector" type="select" label="Reporting options" help="Sets -P --pvar option">
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366 <option value="do_not_set" selected="True">Use defaults</option>
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367 <option value="set">Set reporting options</option>
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368 </param>
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369 <when value="set">
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370 <param name="pvar" type="float" value="0.0" label="Report sites if the probability that there is a polymorphism at the site is greater than"
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371 help="-P --pvar; default=0.0. Note that post-filtering is generally recommended over the use of this parameter. " />
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372 </when>
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373 <when value="do_not_set">
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374 <!-- do nothing -->
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375 </when>
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376 </conditional>
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377 <!-- population model -->
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378 <conditional name="population_model">
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379 <param name="population_model_selector" type="select" label="Population model options"
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380 help="Sets --theta, --ploidy, --pooled-discrete, and --pooled-continuous options " >
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381 <option value="do_not_set" selected="true">Use defaults</option>
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382 <option value="set">Set population model options</option>
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383 </param>
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384 <when value="set">
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385 <param name="T" type="float" value="0.001" label="The expected mutation rate or pairwise nucleotide diversity among the population under analysis"
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386 help="-T --theta; default = 0.001. This serves as the single parameter to the Ewens Sampling Formula prior model." />
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387 <param name="P" type="integer" value="2" label="Set ploidy for the analysis" help="-p --ploidy; default=2" />
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388 <param name="J" type="boolean" truevalue="-J" falsevalue="" checked="False" label="Assume that samples result from pooled sequencing"
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389 help="-J --pooled-discrete; default=False. Model pooled samples using discrete genotypes across pools.
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390 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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391 <param name="K" type="boolean" truevalue="-K" falsevalue="" checked="False" label="Output all alleles which pass input filters, regardles of genotyping outcome or model"
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392 help="-K, --poled-continuous; default=False." />
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393 </when>
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394 <when value="do_not_set">
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395 <!-- do nothing -->
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396 </when>
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397 </conditional>
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398 <!-- reference allele -->
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399 <conditional name="reference_allele">
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400 <param name="reference_allele_selector" type="select" label="Reference allele options"
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401 help="Sets --use-reference-allele and --reference-quality options.">
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402 <option value="do_not_set" selected="true">Use defaults</option>
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403 <option value="set">Set reference allele options</option>
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404 </param>
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405 <when value="set">
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406 <param name="Z" type="boolean" truevalue="-Z" falsevalue="" checked="False" label="Include the reference allele in the analysis as if it is another sample from the same population"
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407 help="-Z --use-reference-allele; default=False" />
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408 <param name="reference_quality" type="text" value="100,60" label="Assign mapping quality of MQ (100) to the reference allele at each site and base quality of BQ (60)"
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409 help="--reference-quality; default=100,60 " />
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410 </when>
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411 <when value="do_not_set">
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412 <!-- do nothing -->
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413 </when>
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414 </conditional>
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415 <!-- allelic scope -->
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416 <conditional name="allele_scope">
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417 <param name="allele_scope_selector" type="select" label="Allelic scope options"
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418 help="Sets -I, i, -X, -u, -n, --haplotype-length, --min-repeat-size, --min-repeat-entropy, and --no-partial-observations options.">
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419 <option value="do_not_set" selected="true">Use defaults</option>
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420 <option value="set">Set alleic scope options</option>
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421 </param>
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422 <when value="set">
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423 <param name="I" type="boolean" truevalue="-I" falsevalue="" checked="False" label="Ignore SNP alleles" help="-I --no-snps; default=False" />
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424 <param name="i" type="boolean" truevalue="-i" falsevalue="" checked="False" label="Ignore indels alleles" help="-i --no-indels; default=False" />
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425 <param name="X" type="boolean" truevalue="-X" falsevalue="" checked="False" label="Ignore multi-nucleotide polymorphisms, MNPs" help="-X --no-mnps; default=False" />
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426 <param name="u" type="boolean" truevalue="-u" falsevalue="" checked="False" label="Ignore complex events (composites of other classes)."
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427 help="-u --no-complex; default=False" />
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428 <param name="n" type="integer" value="0" label="How many best SNP alleles to evaluate"
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429 help="-n --use-best-n-alleles; default=0 (all). Alleles are ranked by the sum of supporting quality scores. Set to 0 to evaluate all" />
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430 <param name="haplotype_length" type="integer" value="3" label="Allow haplotype calls with contiguous embedded matches of up to (nucleotides)"
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431 help="-E --max-complex-gap --haplotype-length; default=3." />
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432 <param name="min_repeat_length" type="integer" value="5" label="When assembling observations across repeats, require the total repeat length at least this many bp"
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433 help="--min-repeat-size; default=5." />
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434 <param name="min_repeat_entropy" type="integer" value="0" label="To detect interrupted repeats, build across sequence until it has entropy > (bits per bp)"
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435 help="--min-repeat-entropy; default=0 (off)." />
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436 <param name="no_partial_observations" type="boolean" truevalue="--no-partial-observations" falsevalue="" checked="False"
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437 label="Exclude observations which do not fully span the dynamically-determined detection window"
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438 help="--no-partial-observations; default=use all observations, dividing partial support across matching haplotypes when generating haplotypes." />
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439 </when>
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440 <when value="do_not_set">
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441 <!-- do nothing -->
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442 </when>
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443 </conditional>
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444 <!-- indel realignment -->
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445 <param name="O" type="boolean" truevalue="-O" falsevalue="" checked="False" label="Turn off left-alignment of indels?"
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446 help="-O --dont-left-align-indels; default=False (do left align)." />
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447 <!-- input filters -->
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448 <conditional name="input_filters">
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449 <param name="input_filters_selector" type="select" label="Input filters"
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450 help="Sets -4, -m, -q, -R, -Y, -Q, -U, -z, -&#36;, -e, -0, -F, -C, -3, -G, and -&#33; options.">
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451 <option value="do_not_set" selected="true">No input filters (default)</option>
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452 <option value="set">Set input filters</option>
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453 </param>
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454 <when value="set">
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455 <param name="use_duplicate_reads" type="boolean" truevalue="--use-duplicate-reads" falsevalue="" checked="False"
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456 label="Include duplicate-marked alignments in the analysis."
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457 help="-4 --use-duplicate-reads; default=False (exclude duplicates marked as such in alignments)." />
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458 <param name="m" type="integer" value="1" label="Exclude alignments from analysis if they have a mapping quality less than"
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459 help="-m --min-mapping-quality; default=1" />
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460 <param name="q" type="integer" value="0" label="Exclude alleles from analysis if their supporting base quality less than"
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461 help="-q --min-base-quality; default=0" />
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462 <param name="R" type="integer" value="0" label="Consider any allele in which the sum of qualities of supporting observations is at least"
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463 help="-R --min-supporting-allele-qsum; default=0" />
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464 <param name="Y" type="integer" value="0" label="Consider any allele in which and the sum of mapping qualities of supporting reads is at least"
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465 help="-Y --min-supporting-mapping-qsum; default=0" />
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466 <conditional name="mismatch_filters">
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467 <param name="mismatch_filters_selector" type="select" label="Mismatch filters"
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468 help="Sets -Q, -U, -z, and &#36; options">
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469 <option value="do_not_set" selected="true">No mismatch filters (default)</option>
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470 <option value="set">Set mismatch filters</option>
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471 </param>
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472 <when value="set">
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473 <param name="Q" type="integer" value="10" label="Count mismatches toward -U (option below) if the base quality of the mismatch is >="
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474 help="-Q --mismatch-base-quality-threshold; default=10" />
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475 <param name="U" type="integer" value="1000" optional="True" label="Exclude reads with more than N mismatches where each mismatch has base quality >= Q (option above)"
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476 help="-U --read-mismatch-limit; default=~unbound" />
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477 <param name="z" type="float" value="1.0" min="0.0" max="1.0"
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478 label="Exclude reads with more than N [0,1] fraction of mismatches where each mismatch has base quality >= Q (second option above)"
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479 help="-z --read-max-mismatch-fraction; default=1.0" />
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480 <param name="read_snp_limit" type="integer"
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481 value="1000" label="Exclude reads with more than N base mismatches, ignoring gaps with quality >= Q (third option abobe)"
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482 help="-$amp; --read-snp-limit N " />
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483 </when>
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484 <when value="do_not_set">
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diff changeset
485 <!-- do nothing -->
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486 </when>
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487 </conditional>
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488 <param name="e" type="integer" value="1000" label="Exclude reads with more than this number of separate gaps"
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489 help="-e --read-snp-limit; default=~unbounded" />
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490 <param name="standard_filters" type="boolean" truevalue="-0" falsevalue="" checked="False" label="Use stringent input base and mapping quality filters"
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491 help="-0 --standard-filters; default=False. Equivalent to -m 30 -q 20 -R 0 -S 0" />
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diff changeset
492 <param name="F" type="float" value="0.2"
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493 label="Require at least this fraction of observations supporting an alternate allele within a single individual in the in order to evaluate the position"
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494 help="-F --min-alternate-fraction; default=0.2" />
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495 <param name="C" type="integer" value="2"
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496 label="Require at least this count of observations supporting an alternate allele within a single individual in order to evaluate the position"
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497 help="-C --min-alternate-count; default=2" />
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498 <param name="min_alternate_qsum" type="integer" value="0"
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499 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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500 help="-3 --min-alternate-qsum; default=0" />
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501 <param name="G" type="integer" value="1"
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502 label="Require at least this count of observations supporting an alternate allele within the total population in order to use the allele in analysis"
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503 help="-G --min-alternate-total N; default=1" />
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504 <param name="min_coverage" type="integer" value="0" label="Require at least this coverage to process a site"
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diff changeset
505 help="-! --min-coverage; default=0 " />
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506 </when>
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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diff changeset
507 <when value="do_not_set">
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508 <!-- do nothing -->
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diff changeset
509 </when>
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diff changeset
510 </conditional>
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diff changeset
511 <!-- population and mappability priors -->
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512 <conditional name="population_mappability_priors">
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diff changeset
513 <param name="population_mappability_priors_selector" type="select" label="Population and mappability priors"
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diff changeset
514 help="Sets -k, -w, -V, and -a options.">
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515 <option value="do_not_set" selected="true">Use defaults</option>
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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516 <option value="set">Set population and mappability priors</option>
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diff changeset
517 </param>
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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diff changeset
518 <when value="set">
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519 <param name="k" type="boolean" truevalue="-k" falsevalue="" checked="False" label="No population priors"
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520 help="-k --no-population-priors; default=False. Equivalent to --pooled-discrete --hwe-priors-off and removal of Ewens Sampling Formula component of priors." />
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521 <param name="w" type="boolean" truevalue="-w" falsevalue="" checked="False"
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diff changeset
522 label="Disable estimation of the probability of the combination arising under HWE given the allele frequency as estimated by observation frequency"
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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523 help="-w --hwe-priors-off; default=False" />
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parents: 22
diff changeset
524 <param name="V" type="boolean" truevalue="-V" falsevalue="" checked="False" label="Disable incorporation of prior expectations about observations"
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525 help="-V --binomial-obs-priors-off; default=False. Uses read placement probability, strand balance probability, and read position (5&#39;'-3&#39;') probability." />
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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526 <param name="a" type="boolean" truevalue="-a" falsevalue="" checked="False"
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527 label="isable use of aggregate probability of observation balance between alleles as a component of the priors"
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528 help="-a --allele-balance-priors-off; default=False " />
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diff changeset
529 </when>
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530 <when value="do_not_set">
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diff changeset
531 <!-- do nothing -->
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diff changeset
532 </when>
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diff changeset
533 </conditional>
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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534 <!-- genotype likelihoods -->
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diff changeset
535 <conditional name="genotype_likelihoods">
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536 <param name="genotype_likelihoods_selector" type="select" label="Genotype likelihood options"
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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diff changeset
537 help="Sets --base-quality-cap, --experimental-gls, and --prob-contamination options.">
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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diff changeset
538 <option value="do_not_set" selected="true">Use defaults</option>
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539 <option value="set">Set genotype likelihood options</option>
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540 </param>
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541 <when value="set">
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542 <param name="base_quality_cap" type="integer" value="0" label="Limit estimated observation quality by capping base quality at" help="--base-quality-cap" />
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543 <param name="experimental_gls" type="boolean" truevalue="--experimental-gls" falsevalue="" checked="False"
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544 label="Generate genotype likelihoods using 'effective base depth' metric qual = 1-BaseQual * 1-MapQual"
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545 help="--experimental-gls; Incorporate partial observations. This is the default when contamination estimates are provided. Optimized for diploid samples." />
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546 <param name="prob_contamination" type="float" value="10e-9" label="An estimate of contamination to use for all samples"
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547 help="--prob-contamination; default=10e-9." />
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548 </when>
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549 <when value="do_not_set">
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diff changeset
550 <!-- do nothing -->
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551 </when>
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552 </conditional>
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diff changeset
553 <!-- algorithmic features -->
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554 <conditional name="algorithmic_features">
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555 <param name="algorithmic_features_selector" type="select" label="Algorithmic features"
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556 help="Sets --report-genotypes-likelihood-max, -B, --genotyping-max-banddepth, -W, -N, S, -j, -H, -D, -= options">
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557 <option value="do_not_set" selected="true">Use defaults</option>
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558 <option value="set">Set algorithmic features</option>
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559 </param>
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560 <when value="set">
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561 <param name="report_genotype_likelihood_max" type="boolean" truevalue="--report-genotype-likelihood-max" falsevalue="" checked="False"
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562 label="Report genotypes using the maximum-likelihood estimate provided from genotype likelihoods."
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563 help="--report-genotype-likelihood-max; default=False" />
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564 <param name="B" type="integer" value="1000" label="Iterate no more than N times during genotyping step"
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565 help="-B --genotyping-max-iterations; default=1000." />
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566 <param name="genotyping_max_banddepth" type="integer" value="6" label="Integrate no deeper than the Nth best genotype by likelihood when genotyping"
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567 help="--genotyping-max-banddepth; default=6" />
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568 <param name="W" type="text" value="1,3"
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569 label="Integrate all genotype combinations in our posterior space which include no more than N (1) samples with their Mth (3) best data likelihood"
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570 help="-W --posterior-integration-limits; default=1,3" />
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571 <param name="N" type="boolean" truevalue="--exclude-unobserved-genotypes" falsevalue="" checked="False"
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572 label="Skip sample genotypings for which the sample has no supporting reads"
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573 help="-N --exclude-unobserved-genotypes; default=False" />
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574 <conditional name="genotype_variant_threshold">
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575 <param name="genotype_variant_threshold_selector" type="select"
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576 label="Limit posterior integration"
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577 help="-S --genotype-variant-threshold">
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578 <option value="do_not_set" selected="true">Do not limit posterior integration</option>
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diff changeset
579 <option value="set">Set posterior integration limit</option>
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580 </param>
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581 <when value="do_not_set">
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582 <!-- do nothing -->
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diff changeset
583 </when>
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584 <when value="set">
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585 <param name="S" value="" type="integer"
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586 label="Limit posterior integration to samples where the second-best genotype likelihood is no more than log(N) from the highest genotype likelihood for the sample."
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587 help="-S --genotype-variant-threshold; default=~unbounded" />
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diff changeset
588 </when>
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diff changeset
589 </conditional>
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diff changeset
590 <param name="j" type="boolean" truevalue="-j" falsevalue="" checked="False" label="Use mapping quality of alleles when calculating data likelihoods"
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591 help="-j --use-mapping-quality; default=False" />
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592 <param name="H" type="boolean" truevalue="-H" falsevalue="" checked="False"
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593 label="Use a weighted sum of base qualities around an indel, scaled by the distance from the indel"
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594 help="-H --harmonic-indel-quality; default=use a minimum Base Quality in flanking sequence." />
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595 <param name="D" type="float" value="0.9" label="Incorporate non-independence of reads by scaling successive observations by this factor during data likelihood calculations"
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596 help="-D --read-dependence-factor; default=0.9." />
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597 <param name="genotype_qualities" type="boolean" truevalue="--genotype-qualities" falsevalue="" checked="False"
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598 label="Calculate the marginal probability of genotypes and report as GQ in each sample field in the VCF output"
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599 help="-= --genotype-qualities; default=False " />
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600 </when>
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diff changeset
601 <when value="do_not_set">
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602 <!-- do nothing -->
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603 </when>
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604 </conditional>
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605 </when>
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606 <when value="simple">
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607 <!-- do nothing -->
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608 </when>
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609 <when value="simple_w_filters">
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610 <!-- add standard-filters to command line -->
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611 <param name="min_coverage" type="integer" value="0" label="Require at least this coverage to process a site" help="-! --min-coverage; default=0 " />
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612 </when>
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613 <when value="naive">
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614 <!-- do nothing build command line using haplotype-length 0 min-alternate-count 1 min-alternate-fraction 0 pooled-continuous report-monomorphic -->
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615 </when>
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616 <when value="naive_w_filters">
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617 <!-- do nothing build command line using haplotype-length 0 min-alternate-count 1 min-alternate-fraction 0 pooled-continuous report-monomorphic standard-filters-->
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618 <param name="min_coverage" type="integer" value="0" label="Require at least this coverage to process a site" help="-! --min-coverage; default=0 " />
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619 </when>
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620 </conditional>
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621 </inputs>
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diff changeset
622 <outputs>
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623 <data format="vcf" name="output_vcf" label="${tool.name} on ${on_string} (variants)" />
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624 <data format="bed" name="output_failed_alleles_bed" label="${tool.name} on ${on_string} (failed alleles)">
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625 <filter>( options_type['options_type_selector'] == 'cline' or options_type['options_type_selector'] == 'full' ) and options_type['optional_inputs']['optional_inputs_selector'] == 'set' and options_type['optional_inputs']['output_failed_alleles_option'] is True</filter>
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626 </data>
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627 <data format="txt" name="output_trace" label="${tool.name} on ${on_string} (trace)">
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628 <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>
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629 </data>
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630 </outputs>
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631 <tests>
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632 <test>
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633 <param name="reference_source_selector" value="history" />
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634 <param name="ref_file" ftype="fasta" value="freebayes-phix174.fasta"/>
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635 <param name="input_bams" ftype="bam" value="freebayes-phix174.bam"/>
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636 <param name="options_type_selector" value="simple"/>
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637 <output name="output_vcf" file="freebayes-phix174-test1.vcf" compare="contains"/>
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638 </test>
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639 <test>
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640 <param name="reference_source_selector" value="history" />
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641 <param name="ref_file" ftype="fasta" value="freebayes-phix174.fasta"/>
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642 <param name="input_bams" ftype="bam" value="freebayes-phix174.bam"/>
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643 <param name="options_type_selector" value="naive_w_filters"/>
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644 <param name="min_coverage" value="14"/>
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645 <output name="output_vcf" file="freebayes-phix174-test2.vcf" compare="contains"/>
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646 </test>
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647 <test>
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648 <param name="reference_source_selector" value="history" />
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649 <param name="ref_file" ftype="fasta" value="freebayes-phix174.fasta"/>
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650 <param name="input_bams" ftype="bam" value="freebayes-phix174.bam"/>
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651 <param name="options_type_selector" value="naive_w_filters"/>
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652 <param name="min_coverage" value="14"/>
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653 <output name="output_vcf" file="freebayes-phix174-test3.vcf" compare="contains"/>
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654 </test>
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655 <test>
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656 <param name="reference_source_selector" value="history" />
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657 <param name="ref_file" ftype="fasta" value="freebayes-phix174.fasta"/>
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658 <param name="input_bams" ftype="bam" value="freebayes-phix174.bam"/>
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659 <param name="options_type_selector" value="full"/>
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660 <param name="population_model_selector" value="set"/>
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661 <param name="P" value="1"/>
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662 <output name="output_vcf" file="freebayes-phix174-test4.vcf" compare="contains"/>
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663 </test>
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664 </tests>
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665 <help>
13
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666 **What it does**
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667
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668 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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669
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670 See https://github.com/ekg/freebayes for details on FreeBayes.
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671
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672 ------
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673
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674 **Description**
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675
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676 Privided BAM file(s) and a reference. FreeBayes will provide VCF output on standard out describing SNPs, indels, and complex variants in samples in the input alignments.
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677
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678 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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679
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680 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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681
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682 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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683
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684 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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685
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686 -------
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687
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688 **Galaxy-specific options**
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689
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690 Galaxy allows six levels of control over FreeBayes options provided by **Choose parameter selection level** menu option. These are:
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691
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692 1. *Simple diploid calling*: The simples possible FreeBayes application. Equvalent of using FreeBayes with only a BAM input and no other parameter options.
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693 2. *Simple diploid calling with filtering and coverage*: Same as #1 plus two additional options: -0 (standard filters: --min-mapping-quality 30 --min-base-quality 20 --min-supporting-allele-qsum 0 --genotype-varinat-threshold 0) and --min-coverage.
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694 3. *Frequency-based pooled calling*: This is equivalent to using FreeBayes with the following options: --haplotype-length 0 --min-alternate-count 1 --min-alternate-fraction 0 --pooled-continuous --report-monomorphic. This is the best choice for calling varinats in mixtures such as viral, bacterial, or organellar genomes.
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695 4. *Frequency-based pooled calling with filtering and coverage*: Same as #3 but adds -0 and --min-coverage like in #2.
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696 5. *Complete list of all options*: Gives you full control by exposing all FreeBayes options as Galaxy widgets.
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697
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698 -----
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699
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700 **FreeBayes options**
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701
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702 .. class:: infomark
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703
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704 Note that each Galaxy parameter widget corresponding to command line flags listed below:
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705
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706 Input and output::
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707
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708 -t --targets FILE
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709 Limit analysis to targets listed in the BED-format FILE.
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710 -r --region chrom:start_position-end_position
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711 Limit analysis to the specified region, 0-base coordinates,
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712 end_position included. Either '-' or '..' maybe used as a separator.
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713 -s --samples FILE
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714 Limit analysis to samples listed (one per line) in the FILE.
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715 By default FreeBayes will analyze all samples in its input
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716 BAM files.
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717 --populations FILE
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718 Each line of FILE should list a sample and a population which
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719 it is part of. The population-based bayesian inference model
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720 will then be partitioned on the basis of the populations.
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721 -A --cnv-map FILE
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722 Read a copy number map from the BED file FILE, which has
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723 the format:
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724 reference sequence, start, end, sample name, copy number
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725 ... for each region in each sample which does not have the
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726 default copy number as set by --ploidy.
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727 --trace FILE Output an algorithmic trace to FILE.
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728 --failed-alleles FILE
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729 Write a BED file of the analyzed positions which do not
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730 pass --pvar to FILE.
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731 -@ --variant-input VCF
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732 Use variants reported in VCF file as input to the algorithm.
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733 Variants in this file will be treated as putative variants
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734 even if there is not enough support in the data to pass
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735 input filters.
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736 -l --only-use-input-alleles
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737 Only provide variant calls and genotype likelihoods for sites
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738 and alleles which are provided in the VCF input, and provide
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739 output in the VCF for all input alleles, not just those which
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740 have support in the data.
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741 --haplotype-basis-alleles VCF
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742 When specified, only variant alleles provided in this input
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743 VCF will be used for the construction of complex or haplotype
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744 alleles.
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745 --report-all-haplotype-alleles
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746 At sites where genotypes are made over haplotype alleles,
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747 provide information about all alleles in output, not only
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748 those which are called.
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749 --report-monomorphic
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750 Report even loci which appear to be monomorphic, and report all
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751 considered alleles, even those which are not in called genotypes.
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752 Loci which do not have any potential alternates have '.' for ALT.
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753
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754 Reporting::
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755
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756 -P --pvar N Report sites if the probability that there is a polymorphism
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757 at the site is greater than N. default: 0.0. Note that post-
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758 filtering is generally recommended over the use of this parameter.
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759
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760 Population model::
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761
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762 -T --theta N The expected mutation rate or pairwise nucleotide diversity
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parents:
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763 among the population under analysis. This serves as the
2dd40b601766 Uploaded
devteam
parents:
diff changeset
764 single parameter to the Ewens Sampling Formula prior model
2dd40b601766 Uploaded
devteam
parents:
diff changeset
765 default: 0.001
2dd40b601766 Uploaded
devteam
parents:
diff changeset
766 -p --ploidy N Sets the default ploidy for the analysis to N. default: 2
2dd40b601766 Uploaded
devteam
parents:
diff changeset
767 -J --pooled-discrete
2dd40b601766 Uploaded
devteam
parents:
diff changeset
768 Assume that samples result from pooled sequencing.
2dd40b601766 Uploaded
devteam
parents:
diff changeset
769 Model pooled samples using discrete genotypes across pools.
2dd40b601766 Uploaded
devteam
parents:
diff changeset
770 When using this flag, set --ploidy to the number of
2dd40b601766 Uploaded
devteam
parents:
diff changeset
771 alleles in each sample or use the --cnv-map to define
2dd40b601766 Uploaded
devteam
parents:
diff changeset
772 per-sample ploidy.
2dd40b601766 Uploaded
devteam
parents:
diff changeset
773 -K --pooled-continuous
2dd40b601766 Uploaded
devteam
parents:
diff changeset
774 Output all alleles which pass input filters, regardles of
2dd40b601766 Uploaded
devteam
parents:
diff changeset
775 genotyping outcome or model.
2dd40b601766 Uploaded
devteam
parents:
diff changeset
776
2dd40b601766 Uploaded
devteam
parents:
diff changeset
777 Reference allele::
2dd40b601766 Uploaded
devteam
parents:
diff changeset
778
2dd40b601766 Uploaded
devteam
parents:
diff changeset
779 -Z --use-reference-allele
2dd40b601766 Uploaded
devteam
parents:
diff changeset
780 This flag includes the reference allele in the analysis as
2dd40b601766 Uploaded
devteam
parents:
diff changeset
781 if it is another sample from the same population.
2dd40b601766 Uploaded
devteam
parents:
diff changeset
782 --reference-quality MQ,BQ
2dd40b601766 Uploaded
devteam
parents:
diff changeset
783 Assign mapping quality of MQ to the reference allele at each
2dd40b601766 Uploaded
devteam
parents:
diff changeset
784 site and base quality of BQ. default: 100,60
2dd40b601766 Uploaded
devteam
parents:
diff changeset
785
2dd40b601766 Uploaded
devteam
parents:
diff changeset
786 Allele scope::
2dd40b601766 Uploaded
devteam
parents:
diff changeset
787
2dd40b601766 Uploaded
devteam
parents:
diff changeset
788 -I --no-snps Ignore SNP alleles.
2dd40b601766 Uploaded
devteam
parents:
diff changeset
789 -i --no-indels Ignore insertion and deletion alleles.
2dd40b601766 Uploaded
devteam
parents:
diff changeset
790 -X --no-mnps Ignore multi-nuceotide polymorphisms, MNPs.
2dd40b601766 Uploaded
devteam
parents:
diff changeset
791 -u --no-complex Ignore complex events (composites of other classes).
2dd40b601766 Uploaded
devteam
parents:
diff changeset
792 -n --use-best-n-alleles N
2dd40b601766 Uploaded
devteam
parents:
diff changeset
793 Evaluate only the best N SNP alleles, ranked by sum of
2dd40b601766 Uploaded
devteam
parents:
diff changeset
794 supporting quality scores. (Set to 0 to use all; default: all)
2dd40b601766 Uploaded
devteam
parents:
diff changeset
795 -E --max-complex-gap N
2dd40b601766 Uploaded
devteam
parents:
diff changeset
796 --haplotype-length N
2dd40b601766 Uploaded
devteam
parents:
diff changeset
797 Allow haplotype calls with contiguous embedded matches of up
2dd40b601766 Uploaded
devteam
parents:
diff changeset
798 to this length. (default: 3)
15
59731e950e23 Fix some options.
soranzo
parents: 13
diff changeset
799 --min-repeat-size N
13
2dd40b601766 Uploaded
devteam
parents:
diff changeset
800 When assembling observations across repeats, require the total repeat
2dd40b601766 Uploaded
devteam
parents:
diff changeset
801 length at least this many bp. (default: 5)
2dd40b601766 Uploaded
devteam
parents:
diff changeset
802 --min-repeat-entropy N
2dd40b601766 Uploaded
devteam
parents:
diff changeset
803 To detect interrupted repeats, build across sequence until it has
2dd40b601766 Uploaded
devteam
parents:
diff changeset
804 entropy > N bits per bp. (default: 0, off)
2dd40b601766 Uploaded
devteam
parents:
diff changeset
805 --no-partial-observations
2dd40b601766 Uploaded
devteam
parents:
diff changeset
806 Exclude observations which do not fully span the dynamically-determined
2dd40b601766 Uploaded
devteam
parents:
diff changeset
807 detection window. (default, use all observations, dividing partial
2dd40b601766 Uploaded
devteam
parents:
diff changeset
808 support across matching haplotypes when generating haplotypes.)
2dd40b601766 Uploaded
devteam
parents:
diff changeset
809
2dd40b601766 Uploaded
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parents:
diff changeset
810 Indel realignment::
2dd40b601766 Uploaded
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parents:
diff changeset
811
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devteam
parents:
diff changeset
812 -O --dont-left-align-indels
2dd40b601766 Uploaded
devteam
parents:
diff changeset
813 Turn off left-alignment of indels, which is enabled by default.
2dd40b601766 Uploaded
devteam
parents:
diff changeset
814
2dd40b601766 Uploaded
devteam
parents:
diff changeset
815 Input filters::
2dd40b601766 Uploaded
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parents:
diff changeset
816
2dd40b601766 Uploaded
devteam
parents:
diff changeset
817 -4 --use-duplicate-reads
2dd40b601766 Uploaded
devteam
parents:
diff changeset
818 Include duplicate-marked alignments in the analysis.
2dd40b601766 Uploaded
devteam
parents:
diff changeset
819 default: exclude duplicates marked as such in alignments
2dd40b601766 Uploaded
devteam
parents:
diff changeset
820 -m --min-mapping-quality Q
2dd40b601766 Uploaded
devteam
parents:
diff changeset
821 Exclude alignments from analysis if they have a mapping
2dd40b601766 Uploaded
devteam
parents:
diff changeset
822 quality less than Q. default: 1
2dd40b601766 Uploaded
devteam
parents:
diff changeset
823 -q --min-base-quality Q
2dd40b601766 Uploaded
devteam
parents:
diff changeset
824 Exclude alleles from analysis if their supporting base
2dd40b601766 Uploaded
devteam
parents:
diff changeset
825 quality is less than Q. default: 0
2dd40b601766 Uploaded
devteam
parents:
diff changeset
826 -R --min-supporting-allele-qsum Q
2dd40b601766 Uploaded
devteam
parents:
diff changeset
827 Consider any allele in which the sum of qualities of supporting
2dd40b601766 Uploaded
devteam
parents:
diff changeset
828 observations is at least Q. default: 0
2dd40b601766 Uploaded
devteam
parents:
diff changeset
829 -Y --min-supporting-mapping-qsum Q
2dd40b601766 Uploaded
devteam
parents:
diff changeset
830 Consider any allele in which and the sum of mapping qualities of
2dd40b601766 Uploaded
devteam
parents:
diff changeset
831 supporting reads is at least Q. default: 0
2dd40b601766 Uploaded
devteam
parents:
diff changeset
832 -Q --mismatch-base-quality-threshold Q
2dd40b601766 Uploaded
devteam
parents:
diff changeset
833 Count mismatches toward --read-mismatch-limit if the base
2dd40b601766 Uploaded
devteam
parents:
diff changeset
834 quality of the mismatch is >= Q. default: 10
2dd40b601766 Uploaded
devteam
parents:
diff changeset
835 -U --read-mismatch-limit N
2dd40b601766 Uploaded
devteam
parents:
diff changeset
836 Exclude reads with more than N mismatches where each mismatch
2dd40b601766 Uploaded
devteam
parents:
diff changeset
837 has base quality >= mismatch-base-quality-threshold.
2dd40b601766 Uploaded
devteam
parents:
diff changeset
838 default: ~unbounded
2dd40b601766 Uploaded
devteam
parents:
diff changeset
839 -z --read-max-mismatch-fraction N
2dd40b601766 Uploaded
devteam
parents:
diff changeset
840 Exclude reads with more than N [0,1] fraction of mismatches where
2dd40b601766 Uploaded
devteam
parents:
diff changeset
841 each mismatch has base quality >= mismatch-base-quality-threshold
2dd40b601766 Uploaded
devteam
parents:
diff changeset
842 default: 1.0
2dd40b601766 Uploaded
devteam
parents:
diff changeset
843 -$ --read-snp-limit N
2dd40b601766 Uploaded
devteam
parents:
diff changeset
844 Exclude reads with more than N base mismatches, ignoring gaps
2dd40b601766 Uploaded
devteam
parents:
diff changeset
845 with quality >= mismatch-base-quality-threshold.
2dd40b601766 Uploaded
devteam
parents:
diff changeset
846 default: ~unbounded
2dd40b601766 Uploaded
devteam
parents:
diff changeset
847 -e --read-indel-limit N
2dd40b601766 Uploaded
devteam
parents:
diff changeset
848 Exclude reads with more than N separate gaps.
2dd40b601766 Uploaded
devteam
parents:
diff changeset
849 default: ~unbounded
2dd40b601766 Uploaded
devteam
parents:
diff changeset
850 -0 --standard-filters Use stringent input base and mapping quality filters
2dd40b601766 Uploaded
devteam
parents:
diff changeset
851 Equivalent to -m 30 -q 20 -R 0 -S 0
2dd40b601766 Uploaded
devteam
parents:
diff changeset
852 -F --min-alternate-fraction N
2dd40b601766 Uploaded
devteam
parents:
diff changeset
853 Require at least this fraction of observations supporting
2dd40b601766 Uploaded
devteam
parents:
diff changeset
854 an alternate allele within a single individual in the
2dd40b601766 Uploaded
devteam
parents:
diff changeset
855 in order to evaluate the position. default: 0.2
2dd40b601766 Uploaded
devteam
parents:
diff changeset
856 -C --min-alternate-count N
2dd40b601766 Uploaded
devteam
parents:
diff changeset
857 Require at least this count of observations supporting
2dd40b601766 Uploaded
devteam
parents:
diff changeset
858 an alternate allele within a single individual in order
2dd40b601766 Uploaded
devteam
parents:
diff changeset
859 to evaluate the position. default: 2
2dd40b601766 Uploaded
devteam
parents:
diff changeset
860 -3 --min-alternate-qsum N
2dd40b601766 Uploaded
devteam
parents:
diff changeset
861 Require at least this sum of quality of observations supporting
2dd40b601766 Uploaded
devteam
parents:
diff changeset
862 an alternate allele within a single individual in order
2dd40b601766 Uploaded
devteam
parents:
diff changeset
863 to evaluate the position. default: 0
2dd40b601766 Uploaded
devteam
parents:
diff changeset
864 -G --min-alternate-total N
2dd40b601766 Uploaded
devteam
parents:
diff changeset
865 Require at least this count of observations supporting
2dd40b601766 Uploaded
devteam
parents:
diff changeset
866 an alternate allele within the total population in order
2dd40b601766 Uploaded
devteam
parents:
diff changeset
867 to use the allele in analysis. default: 1
2dd40b601766 Uploaded
devteam
parents:
diff changeset
868 -! --min-coverage N
2dd40b601766 Uploaded
devteam
parents:
diff changeset
869 Require at least this coverage to process a site. default: 0
2dd40b601766 Uploaded
devteam
parents:
diff changeset
870
2dd40b601766 Uploaded
devteam
parents:
diff changeset
871 Population priors::
2dd40b601766 Uploaded
devteam
parents:
diff changeset
872
2dd40b601766 Uploaded
devteam
parents:
diff changeset
873 -k --no-population-priors
2dd40b601766 Uploaded
devteam
parents:
diff changeset
874 Equivalent to --pooled-discrete --hwe-priors-off and removal of
2dd40b601766 Uploaded
devteam
parents:
diff changeset
875 Ewens Sampling Formula component of priors.
2dd40b601766 Uploaded
devteam
parents:
diff changeset
876
2dd40b601766 Uploaded
devteam
parents:
diff changeset
877 Mappability priors::
2dd40b601766 Uploaded
devteam
parents:
diff changeset
878
2dd40b601766 Uploaded
devteam
parents:
diff changeset
879 -w --hwe-priors-off
2dd40b601766 Uploaded
devteam
parents:
diff changeset
880 Disable estimation of the probability of the combination
2dd40b601766 Uploaded
devteam
parents:
diff changeset
881 arising under HWE given the allele frequency as estimated
2dd40b601766 Uploaded
devteam
parents:
diff changeset
882 by observation frequency.
2dd40b601766 Uploaded
devteam
parents:
diff changeset
883 -V --binomial-obs-priors-off
2dd40b601766 Uploaded
devteam
parents:
diff changeset
884 Disable incorporation of prior expectations about observations.
2dd40b601766 Uploaded
devteam
parents:
diff changeset
885 Uses read placement probability, strand balance probability,
2dd40b601766 Uploaded
devteam
parents:
diff changeset
886 and read position (5'-3') probability.
2dd40b601766 Uploaded
devteam
parents:
diff changeset
887 -a --allele-balance-priors-off
2dd40b601766 Uploaded
devteam
parents:
diff changeset
888 Disable use of aggregate probability of observation balance between alleles
2dd40b601766 Uploaded
devteam
parents:
diff changeset
889 as a component of the priors.
2dd40b601766 Uploaded
devteam
parents:
diff changeset
890
2dd40b601766 Uploaded
devteam
parents:
diff changeset
891 Genotype likelihoods::
2dd40b601766 Uploaded
devteam
parents:
diff changeset
892
2dd40b601766 Uploaded
devteam
parents:
diff changeset
893 --observation-bias FILE
2dd40b601766 Uploaded
devteam
parents:
diff changeset
894 Read length-dependent allele observation biases from FILE.
2dd40b601766 Uploaded
devteam
parents:
diff changeset
895 The format is [length] [alignment efficiency relative to reference]
2dd40b601766 Uploaded
devteam
parents:
diff changeset
896 where the efficiency is 1 if there is no relative observation bias.
2dd40b601766 Uploaded
devteam
parents:
diff changeset
897 --base-quality-cap Q
2dd40b601766 Uploaded
devteam
parents:
diff changeset
898 Limit estimated observation quality by capping base quality at Q.
2dd40b601766 Uploaded
devteam
parents:
diff changeset
899 --experimental-gls
2dd40b601766 Uploaded
devteam
parents:
diff changeset
900 Generate genotype likelihoods using 'effective base depth' metric
2dd40b601766 Uploaded
devteam
parents:
diff changeset
901 qual = 1-BaseQual * 1-MapQual. Incorporate partial observations.
2dd40b601766 Uploaded
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parents:
diff changeset
902 This is the default when contamination estimates are provided.
2dd40b601766 Uploaded
devteam
parents:
diff changeset
903 Optimized for diploid samples.
2dd40b601766 Uploaded
devteam
parents:
diff changeset
904 --prob-contamination F
2dd40b601766 Uploaded
devteam
parents:
diff changeset
905 An estimate of contamination to use for all samples. default: 10e-9
2dd40b601766 Uploaded
devteam
parents:
diff changeset
906 --contamination-estimates FILE
2dd40b601766 Uploaded
devteam
parents:
diff changeset
907 A file containing per-sample estimates of contamination, such as
2dd40b601766 Uploaded
devteam
parents:
diff changeset
908 those generated by VerifyBamID. The format should be:
2dd40b601766 Uploaded
devteam
parents:
diff changeset
909 sample p(read=R|genotype=AR) p(read=A|genotype=AA)
2dd40b601766 Uploaded
devteam
parents:
diff changeset
910 Sample '*' can be used to set default contamination estimates.
2dd40b601766 Uploaded
devteam
parents:
diff changeset
911
2dd40b601766 Uploaded
devteam
parents:
diff changeset
912 Algorithmic features::
2dd40b601766 Uploaded
devteam
parents:
diff changeset
913
2dd40b601766 Uploaded
devteam
parents:
diff changeset
914 --report-genotype-likelihood-max
2dd40b601766 Uploaded
devteam
parents:
diff changeset
915 Report genotypes using the maximum-likelihood estimate provided
2dd40b601766 Uploaded
devteam
parents:
diff changeset
916 from genotype likelihoods.
2dd40b601766 Uploaded
devteam
parents:
diff changeset
917 -B --genotyping-max-iterations N
2dd40b601766 Uploaded
devteam
parents:
diff changeset
918 Iterate no more than N times during genotyping step. default: 1000.
2dd40b601766 Uploaded
devteam
parents:
diff changeset
919 --genotyping-max-banddepth N
2dd40b601766 Uploaded
devteam
parents:
diff changeset
920 Integrate no deeper than the Nth best genotype by likelihood when
2dd40b601766 Uploaded
devteam
parents:
diff changeset
921 genotyping. default: 6.
2dd40b601766 Uploaded
devteam
parents:
diff changeset
922 -W --posterior-integration-limits N,M
2dd40b601766 Uploaded
devteam
parents:
diff changeset
923 Integrate all genotype combinations in our posterior space
2dd40b601766 Uploaded
devteam
parents:
diff changeset
924 which include no more than N samples with their Mth best
2dd40b601766 Uploaded
devteam
parents:
diff changeset
925 data likelihood. default: 1,3.
2dd40b601766 Uploaded
devteam
parents:
diff changeset
926 -N --exclude-unobserved-genotypes
2dd40b601766 Uploaded
devteam
parents:
diff changeset
927 Skip sample genotypings for which the sample has no supporting reads.
2dd40b601766 Uploaded
devteam
parents:
diff changeset
928 -S --genotype-variant-threshold N
2dd40b601766 Uploaded
devteam
parents:
diff changeset
929 Limit posterior integration to samples where the second-best
2dd40b601766 Uploaded
devteam
parents:
diff changeset
930 genotype likelihood is no more than log(N) from the highest
2dd40b601766 Uploaded
devteam
parents:
diff changeset
931 genotype likelihood for the sample. default: ~unbounded
2dd40b601766 Uploaded
devteam
parents:
diff changeset
932 -j --use-mapping-quality
2dd40b601766 Uploaded
devteam
parents:
diff changeset
933 Use mapping quality of alleles when calculating data likelihoods.
2dd40b601766 Uploaded
devteam
parents:
diff changeset
934 -H --harmonic-indel-quality
2dd40b601766 Uploaded
devteam
parents:
diff changeset
935 Use a weighted sum of base qualities around an indel, scaled by the
2dd40b601766 Uploaded
devteam
parents:
diff changeset
936 distance from the indel. By default use a minimum BQ in flanking sequence.
2dd40b601766 Uploaded
devteam
parents:
diff changeset
937 -D --read-dependence-factor N
2dd40b601766 Uploaded
devteam
parents:
diff changeset
938 Incorporate non-independence of reads by scaling successive
2dd40b601766 Uploaded
devteam
parents:
diff changeset
939 observations by this factor during data likelihood
2dd40b601766 Uploaded
devteam
parents:
diff changeset
940 calculations. default: 0.9
2dd40b601766 Uploaded
devteam
parents:
diff changeset
941 -= --genotype-qualities
2dd40b601766 Uploaded
devteam
parents:
diff changeset
942 Calculate the marginal probability of genotypes and report as GQ in
2dd40b601766 Uploaded
devteam
parents:
diff changeset
943 each sample field in the VCF output.
2dd40b601766 Uploaded
devteam
parents:
diff changeset
944
2dd40b601766 Uploaded
devteam
parents:
diff changeset
945
2dd40b601766 Uploaded
devteam
parents:
diff changeset
946 ------
2dd40b601766 Uploaded
devteam
parents:
diff changeset
947
2dd40b601766 Uploaded
devteam
parents:
diff changeset
948 **Citation**
2dd40b601766 Uploaded
devteam
parents:
diff changeset
949
2dd40b601766 Uploaded
devteam
parents:
diff changeset
950 For the underlying tool, please cite `Erik Garrison and Gabor Marth. Haplotype-based variant detection from short-read sequencing &lt;http://arxiv.org/abs/1207.3907&gt;`_.
2dd40b601766 Uploaded
devteam
parents:
diff changeset
951
2dd40b601766 Uploaded
devteam
parents:
diff changeset
952 The initial version of the wrapper was produced by Dan Blankenberg and upgraded by Anton Nekrutenko.
23
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 22
diff changeset
953 TNG was developed by Bjoern Gruening
13
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devteam
parents:
diff changeset
954
23
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 22
diff changeset
955 </help>
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 22
diff changeset
956 <citations>
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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parents: 22
diff changeset
957 <citation type="bibtex">@misc{1207.3907,
16
6d9407020066 Uploaded
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parents: 15
diff changeset
958 Author = {Erik Garrison},
6d9407020066 Uploaded
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parents: 15
diff changeset
959 Title = {Haplotype-based variant detection from short-read sequencing},
6d9407020066 Uploaded
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parents: 15
diff changeset
960 Year = {2012},
6d9407020066 Uploaded
devteam
parents: 15
diff changeset
961 Eprint = {arXiv:1207.3907},
6d9407020066 Uploaded
devteam
parents: 15
diff changeset
962 url = {http://arxiv.org/abs/1207.3907},
6d9407020066 Uploaded
devteam
parents: 15
diff changeset
963 }</citation>
23
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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parents: 22
diff changeset
964 </citations>
13
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parents:
diff changeset
965 </tool>