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annotate freebayes.xml @ 29:156b60c1530f draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 99e8a87a2993ae644df15756044a40a42aa7a05b
author iuc
date Wed, 25 Oct 2017 08:29:45 -0400
parents 977a5301b66d
children ef2c525bd8cd
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156b60c1530f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 99e8a87a2993ae644df15756044a40a42aa7a05b
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1 <tool id="freebayes" name="FreeBayes" version="@DEPENDENCY_VERSION@-0">
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2 <description>bayesian genetic variant detector</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements">
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7 <requirement type="package" version="4.1.3">gawk</requirement>
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8 <requirement type="package" version="20170422">parallel</requirement>
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9 </expand>
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10 <command detect_errors="exit_code"><![CDATA[
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11 ##set up input files
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12
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13 #set $reference_fasta_filename = "localref.fa"
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14
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15 #if str( $reference_source.reference_source_selector ) == "history":
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16 ln -s -f '${reference_source.ref_file}' '${reference_fasta_filename}' &&
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17 samtools faidx '${reference_fasta_filename}' 2>&1 || echo "Error running samtools faidx for FreeBayes" >&2 &&
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18 #else:
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19 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
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20 #end if
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22 #if $reference_source.batchmode.processmode == 'merge':
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23 #set $input_bamfiles = $reference_source.batchmode.input_bams
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24 #else:
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25 #set $input_bamfiles = [ $reference_source.batchmode.input_bams ]
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26 #end if
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28 #for $bam_count, $input_bam in enumerate( $input_bamfiles ):
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29 ln -s -f '${input_bam}' 'b_${bam_count}.bam' &&
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30 ln -s -f '${input_bam.metadata.bam_index}' 'b_${bam_count}.bam.bai' &&
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31 #end for
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33 ## Tabixize optional input_variant_vcf file (for --variant-input option)
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34 #if ( str( $options_type.options_type_selector ) == 'cline' or str( $options_type.options_type_selector ) == 'full' ) and str( $options_type.optional_inputs.optional_inputs_selector ) == 'set' and str( $options_type.optional_inputs.input_variant_type.input_variant_type_selector ) == "provide_vcf":
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35 ln -s -f '${options_type.optional_inputs.input_variant_type.input_variant_vcf}' input_variant_vcf.vcf.gz &&
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36 ln -s -f '${Tabixized_input}' input_variant_vcf.vcf.gz.tbi &&
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37 #end if
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38
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39 ##if the user has specified a region or target file, just use that instead of calculating a set of unique regions
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40 #if str( $target_limit_type.target_limit_type_selector ) == "limit_by_target_file":
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41 ln -s '${target_limit_type.input_target_bed}' regions_all.bed &&
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42 #elif str( $target_limit_type.target_limit_type_selector ) == "limit_by_region":
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43 printf '${target_limit_type.region_chromosome}\t${target_limit_type.region_start}\t${target_limit_type.region_end}' > regions_all.bed &&
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44 #else
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45 ##divide up the regions in the bam file for efficient processing
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46 #for $bam_count, $input_bam in enumerate( $input_bamfiles ):
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47 samtools view -H b_${bam_count}.bam |
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48 grep '^@SQ' |
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49 cut -f 2- |
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50 awk '{ gsub("^SN:","",$1); gsub("^LN:","",$2); print $1"\t0\t"$2; }' >> regions_all.bed &&
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51 #end for
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52 #end if
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54 sort -u regions_all.bed > regions_uniq.bed &&
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55 ## split into even small chunks, this has some disatvantages and will not be used for the moment
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56 ## bedtools makewindows -b regions_uniq.bed -w 10000000 -s 9990000 > regions.bed &&
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58 mkdir vcf_output failed_alleles trace &&
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60 ## Finished setting up inputs
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62 for i in `cat regions_uniq.bed | awk '{print $1":"$2".."$3}'`;
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63 do
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64 echo "
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66 ## COMMAND LINE STARTS HERE
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68 freebayes
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69
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70 --region '\$i'
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71
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72 #for $bam_count, $input_bam in enumerate( $input_bamfiles ):
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73 --bam 'b_${bam_count}.bam'
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74 #end for
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75 --fasta-reference '${reference_fasta_filename}'
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76
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77 ## Outputs
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78 --vcf './vcf_output/part_\$i.vcf'
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79
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80 ##advanced options
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81 #if str( $options_type.options_type_selector ) == "simple":
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82 #pass
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83 #elif str( $options_type.options_type_selector ) == "simple_w_filters":
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84 --standard-filters
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85 --min-coverage ${options_type.min_coverage}
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86 #elif str( $options_type.options_type_selector ) == "naive":
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87 --haplotype-length 0
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88 --min-alternate-count 1
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89 --min-alternate-fraction 0
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90 --pooled-continuous
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91 --report-monomorphic
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92 #elif str( $options_type.options_type_selector ) == "naive_w_filters":
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93 --haplotype-length 0
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94 --min-alternate-count 1
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95 --min-alternate-fraction 0
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96 --pooled-continuous
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97 --report-monomorphic
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98 --standard-filters
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99 --min-coverage ${options_type.min_coverage}
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100 #elif str( $options_type.options_type_selector ) == "full":
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101 #if str( $options_type.optional_inputs.optional_inputs_selector ) == 'set':
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102 ${options_type.optional_inputs.report_monomorphic}
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103
25
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104 #if $options_type.optional_inputs.output_trace_option:
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105 --trace ./trace/part_'\$i'.txt
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106 #end if
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107 #if $options_type.optional_inputs.output_failed_alleles_option:
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108 --failed-alleles ./failed_alleles/part_'\$i'.bed
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109 #end if
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110 #if $options_type.optional_inputs.samples:
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111 --samples '${options_type.optional_inputs.samples}'
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112 #end if
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113 #if $options_type.optional_inputs.populations:
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114 --populations '${options_type.optional_inputs.populations}'
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115 #end if
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116 #if $options_type.optional_inputs.A:
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117 --cnv-map '${options_type.optional_inputs.A}'
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118 #end if
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119 #if str( $options_type.optional_inputs.input_variant_type.input_variant_type_selector ) == "provide_vcf":
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120 --variant-input 'input_variant_vcf.vcf.gz' ## input_variant_vcf.vcf.gz is symlinked to a galaxy-generated dataset in "Tabixize optional input_variant_vcf file" section of the command line above
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121 ${options_type.optional_inputs.input_variant_type.only_use_input_alleles}
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122 #end if
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123 #if $options_type.optional_inputs.haplotype_basis_alleles:
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124 --haplotype-basis-alleles '${options_type.optional_inputs.haplotype_basis_alleles}'
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125 #end if
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126 #if $options_type.optional_inputs.observation_bias:
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127 --observation-bias '${options_type.optional_inputs.observation_bias}'
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128 #end if
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129 #if $options_type.optional_inputs.contamination_estimates:
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130 --contamination-estimates '${options_type.optional_inputs.contamination_estimates}'
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131 #end if
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132 #end if
23
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133
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134 ## REPORTING
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135 #if str( $options_type.reporting.reporting_selector ) == "set":
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136 --pvar ${options_type.reporting.pvar}
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137 #end if
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138 ## POPULATION MODEL
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139 #if str( $options_type.population_model.population_model_selector ) == "set":
28
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140 --theta ${options_type.population_model.T}
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141 --ploidy ${options_type.population_model.P}
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142 ${options_type.population_model.J}
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143 ${options_type.population_model.K}
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144 #end if
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145
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146 ## REFERENCE ALLELE
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147 #if str( $options_type.reference_allele.reference_allele_selector ) == "set":
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148 ${options_type.reference_allele.Z}
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149 --reference-quality '${options_type.reference_allele.reference_quality}'
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150 #end if
13
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151
25
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152 ## ALLELE SCOPE
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153 #if str( $options_type.allele_scope.allele_scope_selector ) == "set":
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154 ${options_type.allele_scope.I}
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155 ${options_type.allele_scope.i}
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156 ${options_type.allele_scope.X}
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157 ${options_type.allele_scope.u}
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158 ${options_type.allele_scope.no_partial_observations}
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159
28
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160 -n ${options_type.allele_scope.n}
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161
28
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162 --haplotype-length ${options_type.allele_scope.haplotype_length}
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163 --min-repeat-size ${options_type.allele_scope.min_repeat_length}
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164 --min-repeat-entropy ${options_type.allele_scope.min_repeat_entropy}
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165 #end if
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166
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167 ## REALIGNMENT
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168 ${options_type.O}
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169
25
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170 ##INPUT FILTERS
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171 #if str( $options_type.input_filters.input_filters_selector ) == "set":
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172 ${options_type.input_filters.use_duplicate_reads}
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173 -m ${options_type.input_filters.m}
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174 -q ${options_type.input_filters.q}
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175 -R ${options_type.input_filters.R}
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176 -Y ${options_type.input_filters.Y}
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177 -e ${options_type.input_filters.e}
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178 -F ${options_type.input_filters.F}
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179 -C ${options_type.input_filters.C}
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180 -G ${options_type.input_filters.G}
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181
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182 #if str( $options_type.input_filters.mismatch_filters.mismatch_filters_selector ) == "set":
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183 -Q ${options_type.input_filters.mismatch_filters.Q}
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184 #if str($options_type.input_filters.mismatch_filters.U)
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185 -U ${options_type.input_filters.mismatch_filters.U}
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186 #end if
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187 -z ${options_type.input_filters.mismatch_filters.z}
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188
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189 --read-snp-limit ${options_type.input_filters.mismatch_filters.read_snp_limit}
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190 #end if
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191
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192 --min-coverage ${options_type.input_filters.min_coverage}
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193 --min-alternate-qsum ${options_type.input_filters.min_alternate_qsum}
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194 #end if
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195
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196 ## POPULATION AND MAPPABILITY PRIORS
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197 #if str( $options_type.population_mappability_priors.population_mappability_priors_selector ) == "set":
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198 ${options_type.population_mappability_priors.k}
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199 ${options_type.population_mappability_priors.w}
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200 ${options_type.population_mappability_priors.V}
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201 ${options_type.population_mappability_priors.a}
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202 #end if
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203
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204 ## GENOTYPE LIKELIHOODS
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205 #if str( $options_type.genotype_likelihoods.genotype_likelihoods_selector ) == "set":
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206 ${$options_type.genotype_likelihoods.experimental_gls}
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207
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208 --base-quality-cap ${$options_type.genotype_likelihoods.base_quality_cap}
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209 --prob-contamination ${$options_type.genotype_likelihoods.prob_contamination}
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210 #end if
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211
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212 ## ALGORITHMIC FEATURES
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213 #if str( $options_type.algorithmic_features.algorithmic_features_selector ) == "set":
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214 -B '${options_type.algorithmic_features.B}'
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215 -W '${options_type.algorithmic_features.W}'
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216 -D '${options_type.algorithmic_features.D}'
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217
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218 #if str($options_type.algorithmic_features.genotype_variant_threshold)
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219 -S ${options_type.algorithmic_features.genotype_variant_threshold}
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220 #end if
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221
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222 ${options_type.algorithmic_features.N}
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223 ${options_type.algorithmic_features.j}
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224 ${options_type.algorithmic_features.H}
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225 ${options_type.algorithmic_features.genotype_qualities}
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226 ${options_type.algorithmic_features.report_genotype_likelihood_max}
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227
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228 --genotyping-max-banddepth ${options_type.algorithmic_features.genotyping_max_banddepth}
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229 #end if
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230 #end if
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231
25
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232 ";
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233 done > freebayes_commands.sh &&
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234
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235 cat freebayes_commands.sh |
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236 parallel --will-cite -j \${GALAXY_SLOTS:-1} &&
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237
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238 ## make VCF header
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239 grep "^#" "./vcf_output/part_\$i.vcf" > header.txt &&
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240
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241 for i in `cat regions_uniq.bed | awk '{print $1":"$2".."$3}'`;
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242 do
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243 ## if this fails then it bails out the script
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244 cat "./vcf_output/part_\$i.vcf" | grep -v "^#" || true
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245 ;
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246 done | sort -k1,1 -k2,2n -k5,5 -u | cat header.txt - > '${output_vcf}'
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247
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248 #if str( $options_type.options_type_selector ) == "full":
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249 #if str( $options_type.optional_inputs.optional_inputs_selector ) == 'set':
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250 #if $options_type.optional_inputs.output_failed_alleles_option:
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251 &&
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252 for i in `cat regions.bed | awk '{print $1":"$2".."$3}'`;
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253 do
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254 cat "./failed_alleles/part_\$i.bed"
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255 ;
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256 done > '${output_failed_alleles_bed}'
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257 #end if
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258
23
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259 #if $options_type.optional_inputs.output_trace_option:
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260 &&
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261 for i in `cat regions.bed | awk '{print $1":"$2".."$3}'`;
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262 do
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263 cat './trace/part_\$i.txt'
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264 ;
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265 done > '${output_trace}'
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266 #end if
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267 #end if
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268 #end if
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269 ]]></command>
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270
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271 <inputs>
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272 <conditional name="reference_source">
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273 <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">
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274 <option value="cached">Locally cached</option>
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275 <option value="history">History</option>
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276 </param>
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277 <when value="cached">
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278 <expand macro="input_bam">
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279 <expand macro="validation" />
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280 </expand>
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281 <param name="ref_file" type="select" label="Using reference genome">
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282 <options from_data_table="fasta_indexes" />
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283 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input dataset"/>
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284 </param>
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285 </when>
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286 <when value="history"> <!-- FIX ME!!!! -->
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287 <expand macro="input_bam" />
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288 <param name="ref_file" type="data" format="fasta" label="Use the following dataset as the reference sequence"
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289 help="You can upload a FASTA sequence to the history and use it as reference" />
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290 </when>
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291 </conditional>
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292 <conditional name="target_limit_type">
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293 <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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294 <option value="do_not_limit" selected="true">Do not limit</option>
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295 <option value="limit_by_target_file">Limit by target file</option>
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296 <option value="limit_by_region">Limit to region</option>
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297 </param>
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298 <when value="do_not_limit" />
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299 <when value="limit_by_target_file">
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300 <param name="input_target_bed" argument="--targets" type="data" format="bed" label="Limit analysis to regions in this BED dataset" />
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301 </when>
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302 <when value="limit_by_region">
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303 <param name="region_chromosome" argument="--region" type="text" label="Region Chromosome" value="" /> <!--only once? -->
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304 <param name="region_start" type="integer" label="Region Start" value="" />
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305 <param name="region_end" type="integer" label="Region End" value="" />
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306 </when>
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307 </conditional>
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308 <conditional name="options_type">
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309 <param name="options_type_selector" type="select" label="Choose parameter selection level"
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310 help="Select how much control over the freebayes run you need">
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311 <option value="simple" selected="true">1. Simple diploid calling</option>
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312 <option value="simple_w_filters">2. Simple diploid calling with filtering and coverage</option>
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313 <option value="naive">3. Frequency-based pooled calling</option>
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314 <option value="naive_w_filters">4. Frequency-based pooled calling with filtering and coverage</option>
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315 <option value="full">5. Full list of options</option>
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316 </param>
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317 <when value="full">
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318 <conditional name="optional_inputs">
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319 <param name="optional_inputs_selector" type="select" label="Additional inputs"
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320 help="Sets --samples, --populations, --cnv-map, --trace, --failed-alleles, --variant-input, --only-use-input-alleles, --haplotype-basis-alleles, --report-all-haplotype-alleles, --report-monomorphic options, --observation-bias, and --contamination-estimates">
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321 <option value="do_not_set" selected="true">Do not provide additional inputs</option>
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322 <option value="set">Provide additional inputs</option>
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323 </param>
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324 <when value="set">
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325 <param name="output_failed_alleles_option" argument="--failed-alleles" type="boolean" truevalue="--failed-alleles" falsevalue="" checked="false"
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326 label="Write out failed alleles file" />
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327 <param name="output_trace_option" argument="--trace" type="boolean" truevalue="--trace" falsevalue="" checked="false"
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328 label="Write out algorithm trace file" />
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329 <param argument="--samples" type="data" format="txt"
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330 label="Limit analysis to samples listed (one per line) in this dataset" optional="true"
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331 help="By default FreeBayes will analyze all samples in its input BAM datasets" />
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332 <param argument="--populations" type="data" format="txt" optional="true"
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333 label="Populations dataset"
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334 help="Each line of this dataset should list a sample and a population which it is part of. The population-based bayesian inference model will then be partitioned on the basis of the populations" />
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335 <param name="A" argument="--cnv-map" type="data" format="bed" optional="true"
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336 label="Read a copy number map from a BED dataset"
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337 help="The BED dataset should have the format: 'reference sequence, start, end, sample name, copy number' for each region in each sample which does not have the default copy number as set by --ploidy. If not specified, copy number is set to as specified by --ploidy" />
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338 <conditional name="input_variant_type">
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339 <param name="input_variant_type_selector" type="select" label="Provide variants dataset">
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340 <option value="do_not_provide" selected="true">Do not provide</option>
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341 <option value="provide_vcf">Provide VCF dataset</option>
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342 </param>
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343 <when value="do_not_provide" />
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344 <when value="provide_vcf">
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345 <param name="input_variant_vcf" argument="--variant-input" type="data" format="vcf_bgzip"
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346 label="Use variants reported in this VCF dataset as input to the algorithm">
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347 <conversion name="Tabixized_input" type="tabix" />
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348 </param>
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349 <param name="only_use_input_alleles" argument="--only-use-input-alleles" type="boolean" truevalue="--only-use-input-alleles" falsevalue="" checked="false"
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350 label="Only provide variant calls and genotype likelihoods for sites in VCF" />
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351 </when>
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352 </conditional>
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353 <param name="haplotype_basis_alleles" argument="--haplotype-basis-alleles" type="data" format="vcf" optional="true"
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354 label="Only use variant alleles provided in this input VCF for the construction of complex or haplotype alleles" />
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355 <param name="report_monomorphic" argument="--report-monomorphic" type="boolean" truevalue="--report-monomorphic" falsevalue="" checked="false"
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356 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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357 <param name="observation_bias" argument="--observation-bias" type="data" format="tabular" optional="true"
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358 label="Load read length-dependent allele observation biases from"
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359 help="The format is [length] [alignment efficiency relative to reference] where the efficiency is 1 if there is no relative observation bias" />
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360 <param name="contamination_estimates" argument="--contamination-estimates" type="data" format="tabular" optional="true"
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diff changeset
361 label="Upload per-sample estimates of contamination from"
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362 help="The format should be: sample p(read=R|genotype=AR) p(read=A|genotype=AA) Sample '*' can be used to set default contamination estimates" />
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363 </when>
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364 <when value="do_not_set" />
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365 </conditional>
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366
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367 <!-- reporting -->
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368 <conditional name="reporting">
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369 <param name="reporting_selector" type="select" label="Reporting options" help="Sets -P --pvar option">
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370 <option value="do_not_set" selected="true">Use defaults</option>
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371 <option value="set">Set reporting options</option>
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372 </param>
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373 <when value="set">
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374 <param argument="--pvar" type="float" value="0.0"
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375 label="Report sites if the probability that there is a polymorphism at the site is greater than"
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376 help="Note that post-filtering is generally recommended over the use of this parameter" />
23
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377 </when>
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378 <when value="do_not_set" />
23
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379 </conditional>
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380
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381 <!-- population model -->
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382 <conditional name="population_model">
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383 <param name="population_model_selector" type="select" label="Population model options"
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384 help="Sets --theta, --ploidy, --pooled-discrete, and --pooled-continuous options">
23
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385 <option value="do_not_set" selected="true">Use defaults</option>
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386 <option value="set">Set population model options</option>
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387 </param>
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388 <when value="set">
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389 <param name="T" argument="--theta" type="float" value="0.001"
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390 label="The expected mutation rate or pairwise nucleotide diversity among the population under analysis"
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391 help="This serves as the single parameter to the Ewens Sampling Formula prior model" />
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392 <param name="P" argument="--ploidy" type="integer" value="2"
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393 label="Set ploidy for the analysis" />
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394 <param name="J" argument="--pooled-discrete" type="boolean" truevalue="-J" falsevalue="" checked="false"
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395 label="Assume that samples result from pooled sequencing"
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396 help="Model pooled samples using discrete genotypes across pools. When using this flag, set --ploidy to the number of alleles in each sample or use the --cnv-map to define per-sample ploidy" />
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397 <param name="K" argument="--poled-continuous" type="boolean" truevalue="-K" falsevalue="" checked="false"
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398 label="Output all alleles which pass input filters, regardles of genotyping outcome or model" />
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399 </when>
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diff changeset
400 <when value="do_not_set" />
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diff changeset
401 </conditional>
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diff changeset
402
23
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diff changeset
403 <!-- reference allele -->
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404 <conditional name="reference_allele">
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405 <param name="reference_allele_selector" type="select" label="Reference allele options"
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406 help="Sets --use-reference-allele and --reference-quality options">
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diff changeset
407 <option value="do_not_set" selected="true">Use defaults</option>
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408 <option value="set">Set reference allele options</option>
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diff changeset
409 </param>
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diff changeset
410 <when value="set">
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411 <param name="Z" argument="--use-reference-allele" type="boolean" truevalue="-Z" falsevalue="" checked="false"
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412 label="Include the reference allele in the analysis as if it is another sample from the same population" />
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413 <param name="reference_quality" argument="--reference-quality" type="text" value="100,60"
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414 label="Assign mapping quality of MQ (100) to the reference allele at each site and base quality of BQ (60)" />
23
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415 </when>
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diff changeset
416 <when value="do_not_set" />
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417 </conditional>
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diff changeset
418
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diff changeset
419 <!-- allelic scope -->
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420 <conditional name="allele_scope">
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421 <param name="allele_scope_selector" type="select" label="Allelic scope options"
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422 help="Sets -I, i, -X, -u, -n, --haplotype-length, --min-repeat-size, --min-repeat-entropy, and --no-partial-observations options">
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423 <option value="do_not_set" selected="true">Use defaults</option>
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diff changeset
424 <option value="set">Set alleic scope options</option>
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diff changeset
425 </param>
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426 <when value="set">
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427 <param name="I" argument="--no-snps" type="boolean" truevalue="-I" falsevalue="" checked="false"
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diff changeset
428 label="Ignore SNP alleles" />
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429 <param name="i" argument="--no-indels" type="boolean" truevalue="-i" falsevalue="" checked="false"
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diff changeset
430 label="Ignore indels alleles" />
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431 <param name="X" argument="--no-mnps" type="boolean" truevalue="-X" falsevalue="" checked="false"
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432 label="Ignore multi-nucleotide polymorphisms, MNPs" />
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433 <param name="u" argument="--no-complex" type="boolean" truevalue="-u" falsevalue="" checked="false"
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434 label="Ignore complex events (composites of other classes)" />
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435 <param name="n" argument="--use-best-n-alleles" type="integer" value="0"
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diff changeset
436 label="How many best SNP alleles to evaluate"
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parents: 27
diff changeset
437 help="Alleles are ranked by the sum of supporting quality scores. Set to 0 to evaluate all" />
977a5301b66d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
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parents: 27
diff changeset
438 <param name="haplotype_length" argument="--haplotype-length" type="integer" value="3"
977a5301b66d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
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parents: 27
diff changeset
439 label="Allow haplotype calls with contiguous embedded matches of up to (nucleotides)" />
977a5301b66d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
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parents: 27
diff changeset
440 <param name="min_repeat_length" argument="--min-repeat-size" type="integer" value="5"
977a5301b66d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 27
diff changeset
441 label="When assembling observations across repeats, require the total repeat length at least this many bp" />
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parents: 27
diff changeset
442 <param name="min_repeat_entropy" argument="--min-repeat-entropy" type="integer" value="0"
977a5301b66d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
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parents: 27
diff changeset
443 label="To detect interrupted repeats, build across sequence until it has entropy > (bits per bp)" />
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parents: 27
diff changeset
444 <param name="no_partial_observations" argument="--no-partial-observations" type="boolean" truevalue="--no-partial-observations" falsevalue="" checked="false"
25
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parents: 24
diff changeset
445 label="Exclude observations which do not fully span the dynamically-determined detection window"
28
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parents: 27
diff changeset
446 help="By default, FreeBayes uses all observations, dividing partial support across matching haplotypes when generating haplotypes" />
23
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parents: 22
diff changeset
447 </when>
28
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parents: 27
diff changeset
448 <when value="do_not_set" />
23
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parents: 22
diff changeset
449 </conditional>
25
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parents: 24
diff changeset
450
23
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parents: 22
diff changeset
451 <!-- indel realignment -->
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parents: 27
diff changeset
452 <param name="O" argument="--dont-left-align-indels" type="boolean" truevalue="-O" falsevalue="" checked="false"
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parents: 27
diff changeset
453 label="Turn off left-alignment of indels" />
25
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parents: 24
diff changeset
454
23
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parents: 22
diff changeset
455 <!-- input filters -->
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parents: 22
diff changeset
456 <conditional name="input_filters">
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parents: 22
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457 <param name="input_filters_selector" type="select" label="Input filters"
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parents: 27
diff changeset
458 help="Sets -4, -m, -q, -R, -Y, -Q, -U, -z, -&#36;, -e, -0, -F, -C, -3, -G, and -&#33; options">
23
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parents: 22
diff changeset
459 <option value="do_not_set" selected="true">No input filters (default)</option>
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parents: 22
diff changeset
460 <option value="set">Set input filters</option>
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parents: 22
diff changeset
461 </param>
25
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iuc
parents: 24
diff changeset
462 <when value="set">
28
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parents: 27
diff changeset
463 <param name="use_duplicate_reads" argument="--use-duplicate-reads" type="boolean" truevalue="--use-duplicate-reads" falsevalue="" checked="false"
977a5301b66d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 27
diff changeset
464 label="Include duplicate-marked alignments in the analysis" />
977a5301b66d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 27
diff changeset
465 <param name="m" argument="--min-mapping-quality" type="integer" value="1"
977a5301b66d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 27
diff changeset
466 label="Exclude alignments from analysis if they have a mapping quality less than" />
977a5301b66d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 27
diff changeset
467 <param name="q" argument="--min-base-quality" type="integer" value="0"
977a5301b66d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 27
diff changeset
468 label="Exclude alleles from analysis if their supporting base quality less than" />
977a5301b66d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 27
diff changeset
469 <param name="R" argument="--min-supporting-allele-qsum" type="integer" value="0"
977a5301b66d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 27
diff changeset
470 label="Consider any allele in which the sum of qualities of supporting observations is at least" />
977a5301b66d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 27
diff changeset
471 <param name="Y" argument="--min-supporting-mapping-qsum" type="integer" value="0"
977a5301b66d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 27
diff changeset
472 label="Consider any allele in which and the sum of mapping qualities of supporting reads is at least" />
23
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parents: 22
diff changeset
473 <conditional name="mismatch_filters">
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parents: 22
diff changeset
474 <param name="mismatch_filters_selector" type="select" label="Mismatch filters"
25
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iuc
parents: 24
diff changeset
475 help="Sets -Q, -U, -z, and &#36; options">
23
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parents: 22
diff changeset
476 <option value="do_not_set" selected="true">No mismatch filters (default)</option>
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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parents: 22
diff changeset
477 <option value="set">Set mismatch filters</option>
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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parents: 22
diff changeset
478 </param>
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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parents: 22
diff changeset
479 <when value="set">
28
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parents: 27
diff changeset
480 <param name="Q" argument="--mismatch-base-quality-threshold" type="integer" value="10"
977a5301b66d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
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parents: 27
diff changeset
481 label="Count mismatches toward -U (option below) if the base quality of the mismatch is >=" />
977a5301b66d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 27
diff changeset
482 <param name="U" type="integer" argument="--read-mismatch-limit" value="1000" optional="true"
977a5301b66d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 27
diff changeset
483 label="Exclude reads with more than N mismatches where each mismatch has base quality >= mismatch-base-quality-threshold (option above)"
977a5301b66d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 27
diff changeset
484 help="default=~unbounded" />
977a5301b66d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 27
diff changeset
485 <param name="z" argument="--read-max-mismatch-fraction" type="float" value="1.0" min="0.0" max="1.0"
977a5301b66d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 27
diff changeset
486 label="Exclude reads with more than N [0,1] fraction of mismatches where each mismatch has base quality >= mismatch-base-quality-threshold (second option above)" />
977a5301b66d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 27
diff changeset
487 <param name="read_snp_limit" argument="--read-snp-limit" type="integer" value="1000"
977a5301b66d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 27
diff changeset
488 label="Exclude reads with more than N base mismatches, ignoring gaps with quality >= mismatch-base-quality-threshold (third option above)"
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parents: 27
diff changeset
489 help="default=~unbounded" />
23
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parents: 22
diff changeset
490 </when>
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parents: 27
diff changeset
491 <when value="do_not_set" />
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diff changeset
492 </conditional>
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parents: 27
diff changeset
493 <param name="e" argument="--read-indel-limit" type="integer" value="1000"
977a5301b66d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
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parents: 27
diff changeset
494 label="Exclude reads with more than this number of separate gaps"
977a5301b66d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
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parents: 27
diff changeset
495 help="default=~unbounded" />
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parents: 27
diff changeset
496 <param name="standard_filters" argument="--standard-filters" type="boolean" truevalue="-0" falsevalue="" checked="false"
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parents: 24
diff changeset
497 label="Use stringent input base and mapping quality filters"
28
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parents: 27
diff changeset
498 help="Equivalent to -m 30 -q 20 -R 0 -S 0" />
977a5301b66d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
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parents: 27
diff changeset
499 <param name="F" argument="--min-alternate-fraction" type="float" value="0.2"
977a5301b66d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
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parents: 27
diff changeset
500 label="Require at least this fraction of observations supporting an alternate allele within a single individual in the in order to evaluate the position" />
977a5301b66d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
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parents: 27
diff changeset
501 <param name="C" argument="--min-alternate-count" type="integer" value="2"
977a5301b66d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 27
diff changeset
502 label="Require at least this count of observations supporting an alternate allele within a single individual in order to evaluate the position" />
977a5301b66d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
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parents: 27
diff changeset
503 <param name="min_alternate_qsum" argument="--min-alternate-qsum" type="integer" value="0"
977a5301b66d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 27
diff changeset
504 label="Require at least this sum of quality of observations supporting an alternate allele within a single individual in order to evaluate the position" />
977a5301b66d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
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parents: 27
diff changeset
505 <param name="G" argument="--min-alternate-total" type="integer" value="1"
977a5301b66d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
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parents: 27
diff changeset
506 label="Require at least this count of observations supporting an alternate allele within the total population in order to use the allele in analysis" />
25
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parents: 24
diff changeset
507 <expand macro="par_min_cov" />
23
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parents: 22
diff changeset
508 </when>
28
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parents: 27
diff changeset
509 <when value="do_not_set" />
23
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parents: 22
diff changeset
510 </conditional>
25
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parents: 24
diff changeset
511
23
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parents: 22
diff changeset
512 <!-- population and mappability priors -->
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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parents: 22
diff changeset
513 <conditional name="population_mappability_priors">
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
514 <param name="population_mappability_priors_selector" type="select" label="Population and mappability priors"
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parents: 27
diff changeset
515 help="Sets -k, -w, -V, and -a options">
23
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parents: 22
diff changeset
516 <option value="do_not_set" selected="true">Use defaults</option>
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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parents: 22
diff changeset
517 <option value="set">Set population and mappability priors</option>
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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parents: 22
diff changeset
518 </param>
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519 <when value="set">
28
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diff changeset
520 <param name="k" argument="--no-population-priors" type="boolean" truevalue="-k" falsevalue="" checked="false"
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diff changeset
521 label="No population priors"
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parents: 27
diff changeset
522 help="Equivalent to --pooled-discrete --hwe-priors-off and removal of Ewens Sampling Formula component of priors" />
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parents: 27
diff changeset
523 <param name="w" argument="--hwe-priors-off" type="boolean" truevalue="-w" falsevalue="" checked="false"
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parents: 27
diff changeset
524 label="Disable estimation of the probability of the combination arising under HWE given the allele frequency as estimated by observation frequency" />
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parents: 27
diff changeset
525 <param name="V" argument="--binomial-obs-priors-off" type="boolean" truevalue="-V" falsevalue="" checked="false"
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parents: 27
diff changeset
526 label="Disable incorporation of prior expectations about observations"
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parents: 27
diff changeset
527 help="Uses read placement probability, strand balance probability, and read position (5&#39;'-3&#39;') probability" />
977a5301b66d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
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parents: 27
diff changeset
528 <param name="a" argument="--allele-balance-priors-off" type="boolean" truevalue="-a" falsevalue="" checked="false"
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parents: 27
diff changeset
529 label="Disable use of aggregate probability of observation balance between alleles as a component of the priors" />
23
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diff changeset
530 </when>
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parents: 27
diff changeset
531 <when value="do_not_set" />
23
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diff changeset
532 </conditional>
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parents: 24
diff changeset
533
23
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diff changeset
534 <!-- genotype likelihoods -->
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diff changeset
535 <conditional name="genotype_likelihoods">
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diff changeset
536 <param name="genotype_likelihoods_selector" type="select" label="Genotype likelihood options"
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diff changeset
537 help="Sets --base-quality-cap, --experimental-gls, and --prob-contamination options">
23
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diff changeset
538 <option value="do_not_set" selected="true">Use defaults</option>
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diff changeset
539 <option value="set">Set genotype likelihood options</option>
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diff changeset
540 </param>
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diff changeset
541 <when value="set">
28
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parents: 27
diff changeset
542 <param name="base_quality_cap" argument="--base-quality-cap" type="integer" value="0"
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parents: 27
diff changeset
543 label="Limit estimated observation quality by capping base quality at" />
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parents: 27
diff changeset
544 <param name="experimental_gls" argument="--experimental-gls" type="boolean" truevalue="--experimental-gls" falsevalue="" checked="false"
25
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parents: 24
diff changeset
545 label="Generate genotype likelihoods using 'effective base depth' metric qual = 1-BaseQual * 1-MapQual"
28
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iuc
parents: 27
diff changeset
546 help="Incorporate partial observations. This is the default when contamination estimates are provided. Optimized for diploid samples" />
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parents: 27
diff changeset
547 <param name="prob_contamination" argument="--prob-contamination" type="float" value="10e-9"
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parents: 27
diff changeset
548 label="An estimate of contamination to use for all samples" />
23
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diff changeset
549 </when>
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parents: 27
diff changeset
550 <when value="do_not_set" />
23
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parents: 22
diff changeset
551 </conditional>
25
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parents: 24
diff changeset
552
23
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parents: 22
diff changeset
553 <!-- algorithmic features -->
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parents: 22
diff changeset
554 <conditional name="algorithmic_features">
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diff changeset
555 <param name="algorithmic_features_selector" type="select" label="Algorithmic features"
25
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parents: 24
diff changeset
556 help="Sets --report-genotypes-likelihood-max, -B, --genotyping-max-banddepth, -W, -N, S, -j, -H, -D, -= options">
23
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parents: 22
diff changeset
557 <option value="do_not_set" selected="true">Use defaults</option>
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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parents: 22
diff changeset
558 <option value="set">Set algorithmic features</option>
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parents: 22
diff changeset
559 </param>
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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parents: 22
diff changeset
560 <when value="set">
28
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parents: 27
diff changeset
561 <param name="report_genotype_likelihood_max" argument="--report-genotype-likelihood-max" type="boolean" truevalue="--report-genotype-likelihood-max" falsevalue="" checked="false"
977a5301b66d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
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parents: 27
diff changeset
562 label="Report genotypes using the maximum-likelihood estimate provided from genotype likelihoods" />
977a5301b66d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 27
diff changeset
563 <param name="B" argument="--genotyping-max-iterations" type="integer" value="1000"
977a5301b66d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 27
diff changeset
564 label="Iterate no more than N times during genotyping step" />
977a5301b66d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 27
diff changeset
565 <param name="genotyping_max_banddepth" argument="--genotyping-max-banddepth" type="integer" value="6"
977a5301b66d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 27
diff changeset
566 label="Integrate no deeper than the Nth best genotype by likelihood when genotyping" />
977a5301b66d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 27
diff changeset
567 <param name="W" argument="--posterior-integration-limits" type="text" value="1,3"
977a5301b66d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 27
diff changeset
568 label="Integrate all genotype combinations in our posterior space which include no more than N (1) samples with their Mth (3) best data likelihood" />
977a5301b66d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
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parents: 27
diff changeset
569 <param name="N" argument="--exclude-unobserved-genotypes" type="boolean" truevalue="--exclude-unobserved-genotypes" falsevalue="" checked="false"
977a5301b66d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 27
diff changeset
570 label="Skip sample genotypings for which the sample has no supporting reads" />
977a5301b66d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 27
diff changeset
571 <param name="genotype_variant_threshold" argument="--genotype-variant-threshold" type="integer" value="" optional="true"
977a5301b66d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 27
diff changeset
572 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"
977a5301b66d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 27
diff changeset
573 help="default=~unbounded" />
977a5301b66d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
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parents: 27
diff changeset
574 <param name="j" argument="--use-mapping-quality" type="boolean" truevalue="-j" falsevalue="" checked="false"
977a5301b66d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 27
diff changeset
575 label="Use mapping quality of alleles when calculating data likelihoods" />
977a5301b66d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
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parents: 27
diff changeset
576 <param name="H" argument="--harmonic-indel-quality" type="boolean" truevalue="-H" falsevalue="" checked="false"
25
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parents: 24
diff changeset
577 label="Use a weighted sum of base qualities around an indel, scaled by the distance from the indel"
28
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parents: 27
diff changeset
578 help="By default, FreeBayes uses a minimum Base Quality in flanking sequence" />
977a5301b66d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
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parents: 27
diff changeset
579 <param name="D" argument="--read-dependence-factor" type="float" value="0.9"
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parents: 27
diff changeset
580 label="Incorporate non-independence of reads by scaling successive observations by this factor during data likelihood calculations" />
977a5301b66d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
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parents: 27
diff changeset
581 <param name="genotype_qualities" argument="--genotype-qualities" type="boolean" truevalue="--genotype-qualities" falsevalue="" checked="false"
977a5301b66d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
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parents: 27
diff changeset
582 label="Calculate the marginal probability of genotypes and report as GQ in each sample field in the VCF output" />
23
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diff changeset
583 </when>
28
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parents: 27
diff changeset
584 <when value="do_not_set" />
23
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parents: 22
diff changeset
585 </conditional>
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diff changeset
586 </when>
28
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parents: 27
diff changeset
587 <when value="simple" />
23
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diff changeset
588 <when value="simple_w_filters">
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diff changeset
589 <!-- add standard-filters to command line -->
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parents: 24
diff changeset
590 <expand macro="par_min_cov" />
23
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parents: 22
diff changeset
591 </when>
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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diff changeset
592 <when value="naive">
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parents: 27
diff changeset
593 <!-- build command line using haplotype-length 0 min-alternate-count 1 min-alternate-fraction 0 pooled-continuous report-monomorphic -->
23
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diff changeset
594 </when>
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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diff changeset
595 <when value="naive_w_filters">
28
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parents: 27
diff changeset
596 <!-- build command line using haplotype-length 0 min-alternate-count 1 min-alternate-fraction 0 pooled-continuous report-monomorphic standard-filters-->
25
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parents: 24
diff changeset
597 <expand macro="par_min_cov" />
23
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parents: 22
diff changeset
598 </when>
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parents: 22
diff changeset
599 </conditional>
52aed7d9ed2b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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diff changeset
600 </inputs>
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601 <outputs>
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602 <data format="vcf" name="output_vcf" label="${tool.name} on ${on_string} (variants)" />
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603 <data format="bed" name="output_failed_alleles_bed" label="${tool.name} on ${on_string} (failed alleles)">
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604 <filter>( options_type['options_type_selector'] == 'cline' or options_type['options_type_selector'] == 'full' ) and options_type['optional_inputs']['optional_inputs_selector'] == 'set' and options_type['optional_inputs']['output_failed_alleles_option'] is True</filter>
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605 </data>
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606 <data format="txt" name="output_trace" label="${tool.name} on ${on_string} (trace)">
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607 <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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608 </data>
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609 </outputs>
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610 <tests>
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611 <test>
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612 <param name="reference_source_selector" value="history" />
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613 <param name="processmode" value="individual" />
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614 <param name="ref_file" ftype="fasta" value="freebayes-phix174.fasta"/>
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615 <param name="input_bams" ftype="bam" value="freebayes-phix174.bam"/>
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616 <param name="options_type_selector" value="simple"/>
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617 <output name="output_vcf" file="freebayes-phix174-test1.vcf" lines_diff="4" />
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618 </test>
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619 <test>
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620 <param name="reference_source_selector" value="history" />
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621 <param name="processmode" value="individual" />
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622 <param name="ref_file" ftype="fasta" value="freebayes-phix174.fasta"/>
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623 <param name="input_bams" ftype="bam" value="freebayes-phix174.bam"/>
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624 <param name="options_type_selector" value="naive_w_filters"/>
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625 <param name="min_coverage" value="14"/>
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626 <output name="output_vcf" file="freebayes-phix174-test2.vcf" lines_diff="4" />
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627 </test>
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628 <test>
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629 <param name="reference_source_selector" value="history" />
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630 <param name="processmode" value="individual" />
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631 <param name="ref_file" ftype="fasta" value="freebayes-phix174.fasta"/>
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632 <param name="input_bams" ftype="bam" value="freebayes-phix174.bam"/>
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633 <param name="options_type_selector" value="naive_w_filters"/>
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634 <param name="min_coverage" value="14"/>
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635 <output name="output_vcf" file="freebayes-phix174-test3.vcf" lines_diff="4" />
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636 </test>
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637 <test>
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638 <param name="reference_source_selector" value="history" />
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639 <param name="processmode" value="individual" />
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640 <param name="ref_file" ftype="fasta" value="freebayes-phix174.fasta"/>
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641 <param name="input_bams" ftype="bam" value="freebayes-phix174.bam"/>
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642 <param name="options_type_selector" value="full"/>
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643 <param name="population_model_selector" value="set"/>
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644 <param name="P" value="1"/>
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645 <output name="output_vcf" file="freebayes-phix174-test4.vcf" lines_diff="4" />
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646 </test>
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647 </tests>
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648 <help>
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649 **What it does**
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650
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651 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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652
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653 See https://github.com/ekg/freebayes for details on FreeBayes.
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654
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655 ------
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656
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657 **Description**
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658
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659 Provided some BAM dataset(s) and a reference sequence, FreeBayes will produce a VCF dataset describing SNPs, indels, and complex variants in samples in the input alignments.
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660
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661 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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662
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663 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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664
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665 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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666
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667 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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668
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669 -------
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670
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671 **Galaxy-specific options**
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672
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673 Galaxy allows five levels of control over FreeBayes options, provided by the **Choose parameter selection level** menu option. These are:
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674
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675 1. *Simple diploid calling*: The simplest possible FreeBayes application. Equivalent to using FreeBayes with only a BAM input and no other parameter options.
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676 2. *Simple diploid calling with filtering and coverage*: Same as #1 plus two additional options: -0 (standard filters: --min-mapping-quality 30 --min-base-quality 20 --min-supporting-allele-qsum 0 --genotype-variant-threshold 0) and --min-coverage.
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677 3. *Frequency-based pooled calling*: This is equivalent to using FreeBayes with the following options: --haplotype-length 0 --min-alternate-count 1 --min-alternate-fraction 0 --pooled-continuous --report-monomorphic. This is the best choice for calling variants in mixtures such as viral, bacterial, or organellar genomes.
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678 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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679 5. *Complete list of all options*: Gives you full control by exposing all FreeBayes options as Galaxy parameters.
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680
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681 ------
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682
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683 **Acknowledgments**
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684
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685 The initial version of the wrapper was produced by Dan Blankenberg and upgraded by Anton Nekrutenko.
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686 TNG was developed by Bjoern Gruening.
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687 </help>
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688 <expand macro="citations">
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689 <citation type="bibtex">
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690 @article{Tange2011a,
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691 title = {GNU Parallel - The Command-Line Power Tool},
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692 author = {O. Tange},
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693 address = {Frederiksberg, Denmark},
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694 journal = {;login: The USENIX Magazine},
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695 month = {Feb},
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696 number = {1},
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697 volume = {36},
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698 url = {http://www.gnu.org/s/parallel},
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699 year = {2011},
156b60c1530f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 99e8a87a2993ae644df15756044a40a42aa7a05b
iuc
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700 pages = {42-47}
156b60c1530f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 99e8a87a2993ae644df15756044a40a42aa7a05b
iuc
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701 }
156b60c1530f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 99e8a87a2993ae644df15756044a40a42aa7a05b
iuc
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702 </citation>
156b60c1530f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 99e8a87a2993ae644df15756044a40a42aa7a05b
iuc
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703 </expand>
13
2dd40b601766 Uploaded
devteam
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704 </tool>