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annotate freebayes.xml @ 7:d0997bd93c49 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 0c59a0b32e4875120e697951a187b81c662bc39c
author iuc
date Thu, 04 May 2017 11:34:00 -0400
parents 3aacf7637e02
children b0ff6447545f
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d0997bd93c49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 0c59a0b32e4875120e697951a187b81c662bc39c
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1 <tool id="freebayes" name="FreeBayes" version="@DEPENDENCY_VERSION@-3">
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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 <requirements>
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7 <requirement type="package" version="@DEPENDENCY_VERSION@">freebayes</requirement>
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8 <requirement type="package" version="0.1.19">samtools</requirement>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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9 <requirement type="package" version="4.1.3">gawk</requirement>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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10 <requirement type="package" version="20160622">parallel</requirement>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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11 </requirements>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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12 <stdio>
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13 <exit_code range="1:" />
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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14 </stdio>
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15 <command><![CDATA[
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16 ##set up input files
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17
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18 #set $reference_fasta_filename = "localref.fa"
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19
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20 #if str( $reference_source.reference_source_selector ) == "history":
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21 ln -s -f '${reference_source.ref_file}' '${reference_fasta_filename}' &&
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
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22 samtools faidx '${reference_fasta_filename}' 2>&1 || echo "Error running samtools faidx for FreeBayes" >&2 &&
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23 #else:
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24 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
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25 #end if
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27 #for $bam_count, $input_bam in enumerate( $reference_source.input_bams ):
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28 ln -s -f '${input_bam}' 'b_${bam_count}.bam' &&
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
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29 ln -s -f '${input_bam.metadata.bam_index}' 'b_${bam_count}.bam.bai' &&
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30 #end for
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31
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32 ## Tabixize optional input_variant_vcf file (for --variant-input option)
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33 #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( $options_type.optional_inputs.input_variant_type.input_variant_type_selector ) == "provide_vcf":
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34 ln -s -f '${options_type.optional_inputs.input_variant_type.input_variant_vcf}' 'input_variant_vcf.vcf.gz' &&
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
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35 ln -s -f '${Tabixized_input}' 'input_variant_vcf.vcf.gz.tbi' &&
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36 #end if
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c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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38 ##if user has specified a region or target file, just use instead of calculating a set of unique regions
d0997bd93c49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 0c59a0b32e4875120e697951a187b81c662bc39c
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d0997bd93c49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 0c59a0b32e4875120e697951a187b81c662bc39c
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40 #if str( $target_limit_type.target_limit_type_selector ) == "limit_by_target_file":
d0997bd93c49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 0c59a0b32e4875120e697951a187b81c662bc39c
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41 ln -s '${target_limit_type.input_target_bed}' regions_all.bed &&
d0997bd93c49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 0c59a0b32e4875120e697951a187b81c662bc39c
iuc
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42 #elif str( $target_limit_type.target_limit_type_selector ) == "limit_by_region":
d0997bd93c49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 0c59a0b32e4875120e697951a187b81c662bc39c
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43 printf '${target_limit_type.region_chromosome}\t${target_limit_type.region_start}\t${target_limit_type.region_end}' > regions_all.bed &&
d0997bd93c49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 0c59a0b32e4875120e697951a187b81c662bc39c
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44 #else
d0997bd93c49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 0c59a0b32e4875120e697951a187b81c662bc39c
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45 ##divide up the regions in the bam file for efficient processing
d0997bd93c49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 0c59a0b32e4875120e697951a187b81c662bc39c
iuc
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46 #for $bam_count, $input_bam in enumerate( $reference_source.input_bams ):
d0997bd93c49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 0c59a0b32e4875120e697951a187b81c662bc39c
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47 samtools view -H b_${bam_count}.bam |
d0997bd93c49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 0c59a0b32e4875120e697951a187b81c662bc39c
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48 grep "^@SQ" |
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49 cut -f 2- |
d0997bd93c49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 0c59a0b32e4875120e697951a187b81c662bc39c
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50 awk '{ gsub("^SN:","",$1);
d0997bd93c49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 0c59a0b32e4875120e697951a187b81c662bc39c
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51 gsub("^LN:","",$2);
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52 print $1"\t0\t"$2; }' >> regions_all.bed &&
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53 #end for
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54 #end if
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58 sort -u regions_all.bed > regions_uniq.bed &&
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59 ## split into even small chunks, this has some disatvantages and will not be used for the moment
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60 ## bedtools makewindows -b regions_uniq.bed -w 10000000 -s 9990000 > regions.bed &&
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62 mkdir vcf_output &&
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63 mkdir failed_alleles &&
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64 mkdir trace &&
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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66 ## Finished setting up inputs
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68 for i in `cat regions_uniq.bed | awk '{print $1":"$2".."$3}'`;
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69 do
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70
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71 echo "
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73 ## COMMAND LINE STARTS HERE
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75 freebayes
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76
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77 --region '\$i'
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79 #for $bam_count, $input_bam in enumerate( $reference_source.input_bams ):
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80 --bam 'b_${bam_count}.bam'
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81 #end for
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82 --fasta-reference '${reference_fasta_filename}'
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83
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84 ## Outputs
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85 --vcf './vcf_output/part_\$i.vcf'
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86
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87 ##advanced options
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88 #if str( $options_type.options_type_selector ) == "simple":
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89 ##do nothing as command like build up to this point is sufficinet for simple diploid calling
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91 #elif str( $options_type.options_type_selector ) == "simple_w_filters":
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92 --standard-filters
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93 --min-coverage '${options_type.min_coverage}'
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94 #elif str( $options_type.options_type_selector ) == "naive":
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95 --haplotype-length 0
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96 --min-alternate-count 1
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97 --min-alternate-fraction 0
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98 --pooled-continuous
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99 --report-monomorphic
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100 #elif str( $options_type.options_type_selector ) == "naive_w_filters":
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101 --haplotype-length 0
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102 --min-alternate-count 1
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103 --min-alternate-fraction 0
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104 --pooled-continuous
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105 --report-monomorphic
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106 --standard-filters
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107 --min-coverage '${options_type.min_coverage}'
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108
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109 ## Command line direct text entry is not allowed at this time for security reasons
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110 #elif str( $options_type.options_type_selector ) == "full":
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111 #if str( $options_type.optional_inputs.optional_inputs_selector ) == 'set':
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112 ${options_type.optional_inputs.report_monomorphic}
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113
6
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114 #if $options_type.optional_inputs.output_trace_option:
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115 --trace ./trace/part_'\$i'.txt
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116 #end if
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117 #if $options_type.optional_inputs.output_failed_alleles_option:
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118 --failed-alleles ./failed_alleles/part_'\$i'.bed
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119 #end if
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120 #if $options_type.optional_inputs.samples:
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121 --samples '${options_type.optional_inputs.samples}'
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122 #end if
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123 #if $options_type.optional_inputs.populations:
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124 --populations '${options_type.optional_inputs.populations}'
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125 #end if
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126 #if $options_type.optional_inputs.A:
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127 --cnv-map '${options_type.optional_inputs.A}'
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128 #end if
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129 #if str( $options_type.optional_inputs.input_variant_type.input_variant_type_selector ) == "provide_vcf":
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130 --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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131 ${options_type.optional_inputs.input_variant_type.only_use_input_alleles}
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132 #end if
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133 #if $options_type.optional_inputs.haplotype_basis_alleles:
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134 --haplotype-basis-alleles '${options_type.optional_inputs.haplotype_basis_alleles}'
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135 #end if
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136 #if $options_type.optional_inputs.observation_bias:
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137 --observation-bias '${options_type.optional_inputs.observation_bias}'
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138 #end if
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139 #if $options_type.optional_inputs.contamination_estimates:
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140 --contamination-estimates '${options_type.optional_inputs.contamination_estimates}'
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141 #end if
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142 #end if
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143
6
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144 ## REPORTING
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145 #if str( $options_type.reporting.reporting_selector ) == "set":
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146 --pvar ${options_type.reporting.pvar}
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147 #end if
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148 ## POPULATION MODEL
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149 #if str( $options_type.population_model.population_model_selector ) == "set":
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150 --theta '${options_type.population_model.T}'
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151 --ploidy '${options_type.population_model.P}'
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152 ${options_type.population_model.J}
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153 ${options_type.population_model.K}
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154 #end if
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155
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156 ## REFERENCE ALLELE
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157 #if str( $options_type.reference_allele.reference_allele_selector ) == "set":
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158 ${options_type.reference_allele.Z}
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159 --reference-quality '${options_type.reference_allele.reference_quality}'
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160 #end if
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161
6
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162 ## ALLELE SCOPE
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163 #if str( $options_type.allele_scope.allele_scope_selector ) == "set":
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164 ${options_type.allele_scope.I}
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165 ${options_type.allele_scope.i}
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166 ${options_type.allele_scope.X}
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167 ${options_type.allele_scope.u}
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168 ${options_type.allele_scope.no_partial_observations}
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169
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170 -n '${options_type.allele_scope.n}'
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171
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172 --haplotype-length '${options_type.allele_scope.haplotype_length}'
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173 --min-repeat-size '${options_type.allele_scope.min_repeat_length}'
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174 --min-repeat-entropy '${options_type.allele_scope.min_repeat_entropy}'
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175 #end if
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176
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177 ## REALIGNMENT
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178 ${options_type.O}
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179
6
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180 ##INPUT FILTERS
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181 #if str( $options_type.input_filters.input_filters_selector ) == "set":
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182 ${options_type.input_filters.use_duplicate_reads}
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183 -m '${options_type.input_filters.m}'
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184 -q '${options_type.input_filters.q}'
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185 -R '${options_type.input_filters.R}'
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186 -Y '${options_type.input_filters.Y}'
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187 -e '${options_type.input_filters.e}'
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188 -F '${options_type.input_filters.F}'
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189 -C '${options_type.input_filters.C}'
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190 -G '${options_type.input_filters.G}'
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191
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192 #if str( $options_type.input_filters.mismatch_filters.mismatch_filters_selector ) == "set":
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193 -Q '${options_type.input_filters.mismatch_filters.Q}'
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194 -U '${options_type.input_filters.mismatch_filters.U}'
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195 -z '${options_type.input_filters.mismatch_filters.z}'
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196
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197 --read-snp-limit '${options_type.input_filters.mismatch_filters.read_snp_limit}'
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198 #end if
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199
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200 --min-coverage '${options_type.input_filters.min_coverage}'
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201 --min-alternate-qsum "${options_type.input_filters.min_alternate_qsum}"
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202 #end if
6
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203
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204 ## POPULATION AND MAPPABILITY PRIORS
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205 #if str( $options_type.population_mappability_priors.population_mappability_priors_selector ) == "set":
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206 ${options_type.population_mappability_priors.k}
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207 ${options_type.population_mappability_priors.w}
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208 ${options_type.population_mappability_priors.V}
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209 ${options_type.population_mappability_priors.a}
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210 #end if
6
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211
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212 ## GENOTYPE LIKELIHOODS
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213 #if str( $options_type.genotype_likelihoods.genotype_likelihoods_selector ) == "set":
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214 ${$options_type.genotype_likelihoods.experimental_gls}
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215
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216 --base-quality-cap '${$options_type.genotype_likelihoods.base_quality_cap}'
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217 --prob-contamination '${$options_type.genotype_likelihoods.prob_contamination}'
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218 #end if
6
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219
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220 ## ALGORITHMIC FEATURES
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221 #if str( $options_type.algorithmic_features.algorithmic_features_selector ) == "set":
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222 -B '${options_type.algorithmic_features.B}'
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223 -W '${options_type.algorithmic_features.W}'
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224 -D '${options_type.algorithmic_features.D}'
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225
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226 #if str( $options_type.algorithmic_features.genotype_variant_threshold.genotype_variant_threshold_selector ) == "set":
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227 -S '${options_type.algorithmic_features.genotype_variant_threshold.S}'
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228 #end if
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229
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230 ${options_type.algorithmic_features.N}
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231 ${options_type.algorithmic_features.j}
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232 ${options_type.algorithmic_features.H}
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233 ${options_type.algorithmic_features.genotype_qualities}
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234 ${options_type.algorithmic_features.report_genotype_likelihood_max}
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235
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236 --genotyping-max-banddepth '${options_type.algorithmic_features.genotyping_max_banddepth}'
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237 #end if
3
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238 #end if
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239
6
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240 ";
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241 done > freebayes_commands.sh &&
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242
6
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243 cat freebayes_commands.sh |
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244 parallel --no-notice -j \${GALAXY_SLOTS:-1} &&
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245
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246 ## make VCF header
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247 grep "^#" "./vcf_output/part_\$i.vcf" > header.txt &&
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248
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249 for i in `cat regions_uniq.bed | awk '{print $1":"$2".."$3}'`;
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250 do
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251 ## if this fails then it bails out the script
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252 cat "./vcf_output/part_\$i.vcf" | grep -v "^#" || true
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253 ;
6
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254 done | sort -k1,1 -k2,2n -k5,5 -u | cat header.txt - > '${output_vcf}'
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255
4
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256 #if str( $options_type.options_type_selector ) == "full":
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257 #if str( $options_type.optional_inputs.optional_inputs_selector ) == 'set':
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258 #if $options_type.optional_inputs.output_failed_alleles_option:
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259 &&
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260 for i in `cat regions.bed | awk '{print $1":"$2".."$3}'`;
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261 do
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262 cat "./failed_alleles/part_\$i.bed"
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263 ;
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264 done > '${output_failed_alleles_bed}'
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265 #end if
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266
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267 #if $options_type.optional_inputs.output_trace_option:
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268 &&
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269 for i in `cat regions.bed | awk '{print $1":"$2".."$3}'`;
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270 do
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271 cat './trace/part_\$i.txt'
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272 ;
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273 done > '${output_trace}'
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274 #end if
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275 #end if
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276 #end if
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277 ]]></command>
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278
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279 <inputs>
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280 <conditional name="reference_source">
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281 <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">
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282 <option value="cached">Locally cached</option>
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283 <option value="history">History</option>
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284 </param>
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285 <when value="cached">
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286 <param name="input_bams" type="data" format="bam" multiple="True" label="BAM file">
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287 <validator type="unspecified_build" />
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288 <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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289 </param>
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290 <param name="ref_file" type="select" label="Using reference genome">
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291 <options from_data_table="fasta_indexes"></options>
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292 <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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293 </param>
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294 </when>
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295 <when value="history"> <!-- FIX ME!!!! -->
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296 <param name="input_bams" type="data" format="bam" multiple="True" label="BAM file" />
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297 <param name="ref_file" type="data" format="fasta" label="Use the following dataset as the reference sequence"
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298 help="You can upload a FASTA sequence to the history and use it as reference" />
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299 </when>
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300 </conditional>
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301 <conditional name="target_limit_type">
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302 <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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303 <option value="do_not_limit" selected="True">Do not limit</option>
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304 <option value="limit_by_target_file">Limit by target file</option>
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305 <option value="limit_by_region">Limit to region</option>
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306 </param>
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307 <when value="do_not_limit" /><!-- Do nothing here -->
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308 <when value="limit_by_target_file">
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309 <param name="input_target_bed" type="data" format="bed" label="Limit analysis to regions in a file (BED-format)." argument="--targets"/>
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310 </when>
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311 <when value="limit_by_region">
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312 <param name="region_chromosome" type="text" label="Region Chromosome" value="" argument="--region"/> <!--only once? -->
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313 <param name="region_start" type="integer" label="Region Start" value="" />
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314 <param name="region_end" type="integer" label="Region End" value="" />
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315 </when>
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316 </conditional>
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317 <conditional name="options_type">
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318 <param name="options_type_selector" type="select" label="Choose parameter selection level"
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319 help="Select how much control over the freebayes run you need" >
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320 <option value="simple" selected="True">1. Simple diploid calling</option>
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321 <option value="simple_w_filters">2. Simple diploid calling with filtering and coverage</option>
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322 <option value="naive">3. Frequency-based pooled calling</option>
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323 <option value="naive_w_filters">4. Frequency-based pooled calling with filtering and coverage</option>
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324 <option value="full">5. Full list of options</option>
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325 </param>
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326 <when value="full">
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327 <conditional name="optional_inputs">
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328 <param name="optional_inputs_selector" type="select" label="Additional inputs"
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329 help="Sets --samples, --populations, --cnv-map, --trace, --failed-alleles, --varinat-input, --only-use-input-alleles, --haplotype-basis-alleles,
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330 --report-all-haplotype-alleles, --report-monomorphic options, --observation-bias, and --contamination-estimates">
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331 <option value="do_not_set" selected="true">Do not provide additional inputs</option>
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332 <option value="set">Provide additional inputs</option>
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333 </param>
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334 <when value="set">
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335 <param name="output_failed_alleles_option" type="boolean" truevalue="--failed-alleles" falsevalue="" checked="False"
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336 label="Write out failed alleles file" argument="--failed-alleles" />
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337 <param name="output_trace_option" type="boolean" truevalue="--trace" falsevalue="" checked="False"
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338 label="Write out algorithm trace file" argument="--trace"/>
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339 <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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340 help="default=By default FreeBayes will analyze all samples in its input BAM files" argument="--samples"/>
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341 <param name="populations" type="data" format="txt" label="Populations File" optional="True"
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342 help="Each line of FILE should list a sample and a population which it is part of. The population-based bayesian inference model will
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343 then be partitioned on the basis of the populations. [default=False]"
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344 argument="--populations" />
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345 <param name="A" type="data" format="bed" label="Read a copy number map from the BED file FILE" optional="True"
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346 help="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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347 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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348 argument="--cnv-map" />
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349 <conditional name="input_variant_type">
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350 <param name="input_variant_type_selector" type="select" label="Provide variants file">
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351 <option value="do_not_provide" selected="True">Do not provide</option>
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352 <option value="provide_vcf">Provide VCF file</option>
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353 </param>
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354 <when value="do_not_provide" /><!-- Do nothing here -->
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355 <when value="provide_vcf">
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356 <param name="input_variant_vcf" type="data" format="vcf_bgzip" label="Use variants reported in VCF file as input to the algorithm" argument="--variant-input">
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357 <conversion name="Tabixized_input" type="tabix" />
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358 </param>
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359 <param name="only_use_input_alleles" type="boolean" truevalue="--only-use-input-alleles" falsevalue="" checked="False"
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360 label="Only provide variant calls and genotype likelihoods for sites in VCF" argument="--only-use-input-alleles" />
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361 </when>
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362 </conditional>
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363 <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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364 argument="--haplotype-basis-alleles" />
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365 <param name="report_monomorphic" type="boolean" truevalue="--report-monomorphic" falsevalue="" checked="False"
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366 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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367 argument="--report-monomorphic" />
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368 <param name="observation_bias" optional="True" type="data" format="tabular" label="Load read length-dependent allele observation biases from"
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369 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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370 argument="--observation-bias" />
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371 <param name="contamination_estimates" optional="True" type="data" format="tabular" label="Upload per-sample estimates of contamination from"
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372 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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373 argument="--contamination-estimates" />
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374 </when>
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375 <when value="do_not_set" /><!-- do nothing -->
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376 </conditional>
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377
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378 <!-- reporting -->
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379 <conditional name="reporting">
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380 <param name="reporting_selector" type="select" label="Reporting options" help="Sets -P --pvar option">
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381 <option value="do_not_set" selected="True">Use defaults</option>
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382 <option value="set">Set reporting options</option>
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383 </param>
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384 <when value="set">
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385 <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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386 help="Note that post-filtering is generally recommended over the use of this parameter. [default=0.0]"
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387 argument="--pvar" />
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388 </when>
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389 <when value="do_not_set" /><!-- do nothing -->
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390 </conditional>
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391
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392 <!-- population model -->
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393 <conditional name="population_model">
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394 <param name="population_model_selector" type="select" label="Population model options"
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395 help="Sets --theta, --ploidy, --pooled-discrete, and --pooled-continuous options " >
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396 <option value="do_not_set" selected="true">Use defaults</option>
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397 <option value="set">Set population model options</option>
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398 </param>
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399 <when value="set">
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400 <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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401 help="This serves as the single parameter to the Ewens Sampling Formula prior model. [default = 0.001]" argument='--theta'/>
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402 <param name="P" type="integer" value="2" label="Set ploidy for the analysis"
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403 help="default=2" argument='--ploidy' />
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404 <param name="J" type="boolean" truevalue="-J" falsevalue="" checked="False" label="Assume that samples result from pooled sequencing"
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405 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. [default=False]"
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406 argument="--pooled-discrete"/>
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407 <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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408 help="default=False." argument="--poled-continuous" />
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409 </when>
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410 <when value="do_not_set" /><!-- do nothing -->
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411 </conditional>
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412
4
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413 <!-- reference allele -->
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414 <conditional name="reference_allele">
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415 <param name="reference_allele_selector" type="select" label="Reference allele options"
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416 help="Sets --use-reference-allele and --reference-quality options.">
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417 <option value="do_not_set" selected="true">Use defaults</option>
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418 <option value="set">Set reference allele options</option>
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419 </param>
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420 <when value="set">
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421 <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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422 help="default=False" argument="--use-reference-allele" />
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423 <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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424 help="default=100,60" argument="--reference-quality" />
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425 </when>
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426 <when value="do_not_set" /><!-- do nothing -->
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427 </conditional>
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428
4
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429 <!-- allelic scope -->
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430 <conditional name="allele_scope">
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431 <param name="allele_scope_selector" type="select" label="Allelic scope options"
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432 help="Sets -I, i, -X, -u, -n, --haplotype-length, --min-repeat-size, --min-repeat-entropy, and --no-partial-observations options.">
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433 <option value="do_not_set" selected="true">Use defaults</option>
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434 <option value="set">Set alleic scope options</option>
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435 </param>
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436 <when value="set">
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437 <param name="I" type="boolean" truevalue="-I" falsevalue="" checked="False" label="Ignore SNP alleles"
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438 help="default=False" argument="--no-snps" />
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439 <param name="i" type="boolean" truevalue="-i" falsevalue="" checked="False" label="Ignore indels alleles"
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440 help="default=False" argument="--no-indels" />
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parents: 5
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441 <param name="X" type="boolean" truevalue="-X" falsevalue="" checked="False" label="Ignore multi-nucleotide polymorphisms, MNPs"
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442 help="default=False" argument="--no-mnps" />
4
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443 <param name="u" type="boolean" truevalue="-u" falsevalue="" checked="False" label="Ignore complex events (composites of other classes)."
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444 help="default=False" argument="--no-complex" />
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445 <param name="n" type="integer" value="0" label="How many best SNP alleles to evaluate"
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446 help="Alleles are ranked by the sum of supporting quality scores. Set to 0 to evaluate all. [default=0 (all)]"
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447 argument="--use-best-n-alleles" />
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448 <param name="haplotype_length" type="integer" value="3" label="Allow haplotype calls with contiguous embedded matches of up to (nucleotides)"
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449 help="-E --max-complex-gap --haplotype-length; default=3." />
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450 <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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451 help="default=5." argument="--min-repeat-size" />
4
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452 <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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453 help="default=0 (off)." argument="--min-repeat-entropy" />
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454 <param name="no_partial_observations" type="boolean" truevalue="--no-partial-observations" falsevalue="" checked="False"
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455 label="Exclude observations which do not fully span the dynamically-determined detection window"
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456 help="default=use all observations, dividing partial support across matching haplotypes when generating haplotypes."
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parents: 5
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457 argument="--no-partial-observations" />
4
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458 </when>
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459 <when value="do_not_set" /><!-- do nothing -->
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460 </conditional>
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461
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462 <!-- indel realignment -->
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parents: 5
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463 <param name="O" type="boolean" truevalue="-O" falsevalue="" checked="False" label="Turn off left-alignment of indels"
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464 help="default=False (do left align)." argument="--dont-left-align-indels" />
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465
4
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diff changeset
466 <!-- input filters -->
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467 <conditional name="input_filters">
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468 <param name="input_filters_selector" type="select" label="Input filters"
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469 help="Sets -4, -m, -q, -R, -Y, -Q, -U, -z, -&#36;, -e, -0, -F, -C, -3, -G, and -&#33; options.">
4
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470 <option value="do_not_set" selected="true">No input filters (default)</option>
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471 <option value="set">Set input filters</option>
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472 </param>
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473 <when value="set">
4
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474 <param name="use_duplicate_reads" type="boolean" truevalue="--use-duplicate-reads" falsevalue="" checked="False"
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475 label="Include duplicate-marked alignments in the analysis."
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476 help="default=False (exclude duplicates marked as such in alignments)." argument="--use-duplicate-reads" />
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477 <param name="m" type="integer" value="1" label="Exclude alignments from analysis if they have a mapping quality less than"
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diff changeset
478 help="default=1" argument="--min-mapping-quality" />
4
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479 <param name="q" type="integer" value="0" label="Exclude alleles from analysis if their supporting base quality less than"
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parents: 5
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480 help="default=0" argument="--min-base-quality" />
4
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481 <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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parents: 5
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482 help="default=0" argument="--min-supporting-allele-qsum" />
4
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483 <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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parents: 5
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484 help="default=0" argument="--min-supporting-mapping-qsum" />
4
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485 <conditional name="mismatch_filters">
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486 <param name="mismatch_filters_selector" type="select" label="Mismatch filters"
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487 help="Sets -Q, -U, -z, and &#36; options">
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488 <option value="do_not_set" selected="true">No mismatch filters (default)</option>
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489 <option value="set">Set mismatch filters</option>
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490 </param>
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491 <when value="set">
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492 <param name="Q" type="integer" value="10"
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493 label="Count mismatches toward -U (option below) if the base quality of the mismatch is >="
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494 help="default=10" argument="--mismatch-base-quality-threshold" />
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495 <param name="U" type="integer" value="1000" optional="True"
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496 label="Exclude reads with more than N mismatches where each mismatch has base quality >= Q (option above)"
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497 help="default=~unbound" argument="--read-mismatch-limit" />
4
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498 <param name="z" type="float" value="1.0" min="0.0" max="1.0"
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499 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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500 help="default=1.0" argument="--read-max-mismatch-fraction" />
4
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501 <param name="read_snp_limit" type="integer"
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502 value="1000" label="Exclude reads with more than N base mismatches, ignoring gaps with quality >= Q (third option abobe)"
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503 argument="--read-snp-limit" />
4
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504 </when>
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parents: 5
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505 <when value="do_not_set" /><!-- do nothing -->
4
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506 </conditional>
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507 <param name="e" type="integer" value="1000" label="Exclude reads with more than this number of separate gaps"
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parents: 5
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508 help="default=~unbounded" argument="--read-snp-limit" />
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509 <param name="standard_filters" type="boolean" truevalue="-0" falsevalue="" checked="False"
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diff changeset
510 label="Use stringent input base and mapping quality filters"
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511 help="default=False. Equivalent to -m 30 -q 20 -R 0 -S 0" argument="--standard-filters"/>
4
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512 <param name="F" type="float" value="0.2"
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diff changeset
513 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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514 help="default=0.2" argument="--min-alternate-fraction" />
4
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diff changeset
515 <param name="C" type="integer" value="2"
6
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iuc
parents: 5
diff changeset
516 label="Require at least this count of observations supporting an alternate allele within a single individual in order to evaluate the position"
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
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parents: 5
diff changeset
517 help="default=2" argument="--min-alternate-count" />
4
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parents: 3
diff changeset
518 <param name="min_alternate_qsum" type="integer" value="0"
6
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parents: 5
diff changeset
519 label="Require at least this sum of quality of observations supporting an alternate allele within a single individual in order to evaluate the position"
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parents: 5
diff changeset
520 help="default=0" argument="--min-alternate-qsum" />
4
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parents: 3
diff changeset
521 <param name="G" type="integer" value="1"
6
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iuc
parents: 5
diff changeset
522 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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iuc
parents: 5
diff changeset
523 help="default=1" argument="--min-alternate-total" />
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iuc
parents: 5
diff changeset
524 <expand macro="par_min_cov" />
4
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parents: 3
diff changeset
525 </when>
6
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iuc
parents: 5
diff changeset
526 <when value="do_not_set" /><!-- do nothing -->
4
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parents: 3
diff changeset
527 </conditional>
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parents: 5
diff changeset
528
4
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parents: 3
diff changeset
529 <!-- population and mappability priors -->
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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parents: 3
diff changeset
530 <conditional name="population_mappability_priors">
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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parents: 3
diff changeset
531 <param name="population_mappability_priors_selector" type="select" label="Population and mappability priors"
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parents: 3
diff changeset
532 help="Sets -k, -w, -V, and -a options.">
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parents: 3
diff changeset
533 <option value="do_not_set" selected="true">Use defaults</option>
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parents: 3
diff changeset
534 <option value="set">Set population and mappability priors</option>
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parents: 3
diff changeset
535 </param>
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parents: 3
diff changeset
536 <when value="set">
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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parents: 3
diff changeset
537 <param name="k" type="boolean" truevalue="-k" falsevalue="" checked="False" label="No population priors"
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parents: 5
diff changeset
538 help="default=False. Equivalent to --pooled-discrete --hwe-priors-off and removal of Ewens Sampling Formula component of priors."
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parents: 5
diff changeset
539 argument="--no-population-priors" />
4
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parents: 3
diff changeset
540 <param name="w" type="boolean" truevalue="-w" falsevalue="" checked="False"
6
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parents: 5
diff changeset
541 label="Disable estimation of the probability of the combination arising under HWE given the allele frequency as estimated by observation frequency"
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
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parents: 5
diff changeset
542 help="default=False" argument="--hwe-priors-off" />
4
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parents: 3
diff changeset
543 <param name="V" type="boolean" truevalue="-V" falsevalue="" checked="False" label="Disable incorporation of prior expectations about observations"
6
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parents: 5
diff changeset
544 help="default=False. Uses read placement probability, strand balance probability, and read position (5&#39;'-3&#39;') probability."
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
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parents: 5
diff changeset
545 argument="--binomial-obs-priors-off" />
4
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parents: 3
diff changeset
546 <param name="a" type="boolean" truevalue="-a" falsevalue="" checked="False"
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iuc
parents: 5
diff changeset
547 label="Disable use of aggregate probability of observation balance between alleles as a component of the priors"
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
548 help="default=False"
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
549 argument="--allele-balance-priors-off" />
4
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parents: 3
diff changeset
550 </when>
6
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iuc
parents: 5
diff changeset
551 <when value="do_not_set" /><!-- do nothing -->
4
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parents: 3
diff changeset
552 </conditional>
6
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parents: 5
diff changeset
553
4
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parents: 3
diff changeset
554 <!-- genotype likelihoods -->
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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parents: 3
diff changeset
555 <conditional name="genotype_likelihoods">
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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parents: 3
diff changeset
556 <param name="genotype_likelihoods_selector" type="select" label="Genotype likelihood options"
6
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parents: 5
diff changeset
557 help="Sets --base-quality-cap, --experimental-gls, and --prob-contamination options.">
4
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parents: 3
diff changeset
558 <option value="do_not_set" selected="true">Use defaults</option>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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parents: 3
diff changeset
559 <option value="set">Set genotype likelihood options</option>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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parents: 3
diff changeset
560 </param>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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parents: 3
diff changeset
561 <when value="set">
6
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iuc
parents: 5
diff changeset
562 <param name="base_quality_cap" type="integer" value="0" label="Limit estimated observation quality by capping base quality at"
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
563 argument="--base-quality-cap" />
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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parents: 3
diff changeset
564 <param name="experimental_gls" type="boolean" truevalue="--experimental-gls" falsevalue="" checked="False"
6
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iuc
parents: 5
diff changeset
565 label="Generate genotype likelihoods using 'effective base depth' metric qual = 1-BaseQual * 1-MapQual"
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
566 help="Incorporate partial observations. This is the default when contamination estimates are provided. Optimized for diploid samples."
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
567 argument="--experimental-gls" />
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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parents: 3
diff changeset
568 <param name="prob_contamination" type="float" value="10e-9" label="An estimate of contamination to use for all samples"
6
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iuc
parents: 5
diff changeset
569 help="default=10e-9." argument="--prob-contamination" />
4
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parents: 3
diff changeset
570 </when>
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
571 <when value="do_not_set" /><!-- do nothing -->
4
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parents: 3
diff changeset
572 </conditional>
6
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parents: 5
diff changeset
573
4
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parents: 3
diff changeset
574 <!-- algorithmic features -->
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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parents: 3
diff changeset
575 <conditional name="algorithmic_features">
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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parents: 3
diff changeset
576 <param name="algorithmic_features_selector" type="select" label="Algorithmic features"
6
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iuc
parents: 5
diff changeset
577 help="Sets --report-genotypes-likelihood-max, -B, --genotyping-max-banddepth, -W, -N, S, -j, -H, -D, -= options">
4
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parents: 3
diff changeset
578 <option value="do_not_set" selected="true">Use defaults</option>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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parents: 3
diff changeset
579 <option value="set">Set algorithmic features</option>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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parents: 3
diff changeset
580 </param>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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parents: 3
diff changeset
581 <when value="set">
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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parents: 3
diff changeset
582 <param name="report_genotype_likelihood_max" type="boolean" truevalue="--report-genotype-likelihood-max" falsevalue="" checked="False"
6
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iuc
parents: 5
diff changeset
583 label="Report genotypes using the maximum-likelihood estimate provided from genotype likelihoods."
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
584 help="default=False" argument="--report-genotype-likelihood-max" />
4
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parents: 3
diff changeset
585 <param name="B" type="integer" value="1000" label="Iterate no more than N times during genotyping step"
6
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iuc
parents: 5
diff changeset
586 help="default=1000." argument="--genotyping-max-iterations" />
4
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parents: 3
diff changeset
587 <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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iuc
parents: 5
diff changeset
588 help="default=6" argument="--genotyping-max-banddepth" />
4
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parents: 3
diff changeset
589 <param name="W" type="text" value="1,3"
6
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iuc
parents: 5
diff changeset
590 label="Integrate all genotype combinations in our posterior space which include no more than N (1) samples with their Mth (3) best data likelihood"
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
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parents: 5
diff changeset
591 help="default=1,3" argument="--posterior-integration-limits" />
4
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parents: 3
diff changeset
592 <param name="N" type="boolean" truevalue="--exclude-unobserved-genotypes" falsevalue="" checked="False"
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iuc
parents: 5
diff changeset
593 label="Skip sample genotypings for which the sample has no supporting reads"
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
594 help="default=False" argument="--exclude-unobserved-genotypes" />
4
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parents: 3
diff changeset
595 <conditional name="genotype_variant_threshold">
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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parents: 3
diff changeset
596 <param name="genotype_variant_threshold_selector" type="select"
6
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597 label="Limit posterior integration" argument="--genotype-variant-threshold">
4
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598 <option value="do_not_set" selected="true">Do not limit posterior integration</option>
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599 <option value="set">Set posterior integration limit</option>
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600 </param>
6
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601 <when value="do_not_set" /><!-- do nothing -->
4
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602 <when value="set">
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603 <param name="S" value="" type="integer"
6
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604 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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605 help="default=~unbounded" argument="--genotype-variant-threshold" />
4
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606 </when>
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607 </conditional>
6
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608 <param name="j" type="boolean" truevalue="-j" falsevalue="" checked="False"
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609 label="Use mapping quality of alleles when calculating data likelihoods"
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610 help="default=False" argument="--use-mapping-quality" />
4
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611 <param name="H" type="boolean" truevalue="-H" falsevalue="" checked="False"
6
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612 label="Use a weighted sum of base qualities around an indel, scaled by the distance from the indel"
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613 help="default=use a minimum Base Quality in flanking sequence." argument="--harmonic-indel-quality" />
4
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614 <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"
6
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615 help="default=0.9." argument="--read-dependence-factor" />
4
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616 <param name="genotype_qualities" type="boolean" truevalue="--genotype-qualities" falsevalue="" checked="False"
6
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617 label="Calculate the marginal probability of genotypes and report as GQ in each sample field in the VCF output"
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618 help="-= --genotype-qualities; default=False " />
4
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619 </when>
6
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620 <when value="do_not_set" /><!-- do nothing -->
4
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621 </conditional>
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622 </when>
6
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623 <when value="simple" /><!-- do nothing -->
4
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624 <when value="simple_w_filters">
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625 <!-- add standard-filters to command line -->
6
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626 <expand macro="par_min_cov" />
4
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627 </when>
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628 <when value="naive">
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629 <!-- do nothing build command line using haplotype-length 0 min-alternate-count 1 min-alternate-fraction 0 pooled-continuous report-monomorphic -->
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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630 </when>
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631 <when value="naive_w_filters">
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632 <!-- do nothing build command line using haplotype-length 0 min-alternate-count 1 min-alternate-fraction 0 pooled-continuous report-monomorphic standard-filters-->
6
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633 <expand macro="par_min_cov" />
4
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634 </when>
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635 </conditional>
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diff changeset
636 </inputs>
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637 <outputs>
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638 <data format="vcf" name="output_vcf" label="${tool.name} on ${on_string} (variants)" />
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639 <data format="bed" name="output_failed_alleles_bed" label="${tool.name} on ${on_string} (failed alleles)">
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640 <filter>( options_type['options_type_selector'] == 'cline' or options_type['options_type_selector'] == 'full' ) and options_type['optional_inputs']['optional_inputs_selector'] == 'set' and options_type['optional_inputs']['output_failed_alleles_option'] is True</filter>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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641 </data>
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642 <data format="txt" name="output_trace" label="${tool.name} on ${on_string} (trace)">
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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643 <filter>( options_type['options_type_selector'] == 'cline' or options_type['options_type_selector'] == 'full' ) and options_type['optional_inputs']['optional_inputs_selector'] == 'set' and options_type['optional_inputs']['output_trace_option'] is True</filter>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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diff changeset
644 </data>
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diff changeset
645 </outputs>
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diff changeset
646 <tests>
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diff changeset
647 <test>
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648 <param name="reference_source_selector" value="history" />
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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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"/>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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651 <param name="options_type_selector" value="simple"/>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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652 <output name="output_vcf" file="freebayes-phix174-test1.vcf" compare="contains"/>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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653 </test>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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654 <test>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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parents: 3
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655 <param name="reference_source_selector" value="history" />
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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656 <param name="ref_file" ftype="fasta" value="freebayes-phix174.fasta"/>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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657 <param name="input_bams" ftype="bam" value="freebayes-phix174.bam"/>
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658 <param name="options_type_selector" value="naive_w_filters"/>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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659 <param name="min_coverage" value="14"/>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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660 <output name="output_vcf" file="freebayes-phix174-test2.vcf" compare="contains"/>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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661 </test>
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662 <test>
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663 <param name="reference_source_selector" value="history" />
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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664 <param name="ref_file" ftype="fasta" value="freebayes-phix174.fasta"/>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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665 <param name="input_bams" ftype="bam" value="freebayes-phix174.bam"/>
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666 <param name="options_type_selector" value="naive_w_filters"/>
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667 <param name="min_coverage" value="14"/>
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668 <output name="output_vcf" file="freebayes-phix174-test3.vcf" compare="contains"/>
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669 </test>
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670 <test>
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671 <param name="reference_source_selector" value="history" />
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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672 <param name="ref_file" ftype="fasta" value="freebayes-phix174.fasta"/>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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673 <param name="input_bams" ftype="bam" value="freebayes-phix174.bam"/>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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674 <param name="options_type_selector" value="full"/>
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675 <param name="population_model_selector" value="set"/>
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diff changeset
676 <param name="P" value="1"/>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
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diff changeset
677 <output name="output_vcf" file="freebayes-phix174-test4.vcf" compare="contains"/>
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678 </test>
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diff changeset
679 </tests>
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680 <help>
0
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681 **What it does**
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682
2
14f952d2a9db Uploaded
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683 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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684
2
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685 See https://github.com/ekg/freebayes for details on FreeBayes.
0
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686
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687 ------
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688
2
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689 **Description**
0
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690
2
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691 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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692
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693 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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694
2
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695 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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696
2
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697 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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698
2
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699 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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700
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701 -------
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702
2
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diff changeset
703 **Galaxy-specific options**
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704
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
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705 Galaxy allows five levels of control over FreeBayes options provided by **Choose parameter selection level** menu option. These are:
0
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706
2
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707 1. *Simple diploid calling*: The simples possible FreeBayes application. Equvalent of using FreeBayes with only a BAM input and no other parameter options.
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
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708 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.
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
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709 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.
2
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710 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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711 5. *Complete list of all options*: Gives you full control by exposing all FreeBayes options as Galaxy widgets.
0
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712
2
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713 -----
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714
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715 **FreeBayes options**
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716
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717 .. class:: infomark
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718
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719 Note that each Galaxy parameter widget corresponding to command line flags listed below:
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720
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721 Input and output::
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722
0
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723 -t --targets FILE
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724 Limit analysis to targets listed in the BED-format FILE.
2
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725 -r --region chrom:start_position-end_position
0
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726 Limit analysis to the specified region, 0-base coordinates,
2
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727 end_position included. Either '-' or '..' maybe used as a separator.
0
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728 -s --samples FILE
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729 Limit analysis to samples listed (one per line) in the FILE.
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730 By default FreeBayes will analyze all samples in its input
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731 BAM files.
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732 --populations FILE
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733 Each line of FILE should list a sample and a population which
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734 it is part of. The population-based bayesian inference model
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735 will then be partitioned on the basis of the populations.
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736 -A --cnv-map FILE
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737 Read a copy number map from the BED file FILE, which has
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738 the format:
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739 reference sequence, start, end, sample name, copy number
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740 ... for each region in each sample which does not have the
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741 default copy number as set by --ploidy.
2
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742 --trace FILE Output an algorithmic trace to FILE.
0
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743 --failed-alleles FILE
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744 Write a BED file of the analyzed positions which do not
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745 pass --pvar to FILE.
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746 -@ --variant-input VCF
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747 Use variants reported in VCF file as input to the algorithm.
2
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748 Variants in this file will be treated as putative variants
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749 even if there is not enough support in the data to pass
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750 input filters.
0
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751 -l --only-use-input-alleles
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752 Only provide variant calls and genotype likelihoods for sites
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753 and alleles which are provided in the VCF input, and provide
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754 output in the VCF for all input alleles, not just those which
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755 have support in the data.
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756 --haplotype-basis-alleles VCF
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757 When specified, only variant alleles provided in this input
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758 VCF will be used for the construction of complex or haplotype
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759 alleles.
2
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760 --report-all-haplotype-alleles
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761 At sites where genotypes are made over haplotype alleles,
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762 provide information about all alleles in output, not only
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763 those which are called.
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764 --report-monomorphic
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765 Report even loci which appear to be monomorphic, and report all
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766 considered alleles, even those which are not in called genotypes.
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767 Loci which do not have any potential alternates have '.' for ALT.
0
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768
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769 Reporting::
0
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770
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771 -P --pvar N Report sites if the probability that there is a polymorphism
2
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772 at the site is greater than N. default: 0.0. Note that post-
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773 filtering is generally recommended over the use of this parameter.
0
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774
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775 Population model::
0
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776
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777 -T --theta N The expected mutation rate or pairwise nucleotide diversity
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778 among the population under analysis. This serves as the
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779 single parameter to the Ewens Sampling Formula prior model
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780 default: 0.001
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781 -p --ploidy N Sets the default ploidy for the analysis to N. default: 2
2
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782 -J --pooled-discrete
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783 Assume that samples result from pooled sequencing.
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784 Model pooled samples using discrete genotypes across pools.
0
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785 When using this flag, set --ploidy to the number of
2
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786 alleles in each sample or use the --cnv-map to define
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787 per-sample ploidy.
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788 -K --pooled-continuous
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789 Output all alleles which pass input filters, regardles of
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790 genotyping outcome or model.
0
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791
2
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792 Reference allele::
0
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793
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794 -Z --use-reference-allele
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795 This flag includes the reference allele in the analysis as
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796 if it is another sample from the same population.
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797 --reference-quality MQ,BQ
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798 Assign mapping quality of MQ to the reference allele at each
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799 site and base quality of BQ. default: 100,60
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800
2
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801 Allele scope::
0
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802
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803 -I --no-snps Ignore SNP alleles.
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804 -i --no-indels Ignore insertion and deletion alleles.
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805 -X --no-mnps Ignore multi-nuceotide polymorphisms, MNPs.
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806 -u --no-complex Ignore complex events (composites of other classes).
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807 -n --use-best-n-alleles N
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808 Evaluate only the best N SNP alleles, ranked by sum of
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809 supporting quality scores. (Set to 0 to use all; default: all)
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810 -E --max-complex-gap N
2
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811 --haplotype-length N
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812 Allow haplotype calls with contiguous embedded matches of up
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813 to this length. (default: 3)
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814 --min-repeat-size N
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815 When assembling observations across repeats, require the total repeat
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816 length at least this many bp. (default: 5)
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817 --min-repeat-entropy N
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818 To detect interrupted repeats, build across sequence until it has
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819 entropy > N bits per bp. (default: 0, off)
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820 --no-partial-observations
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821 Exclude observations which do not fully span the dynamically-determined
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822 detection window. (default, use all observations, dividing partial
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823 support across matching haplotypes when generating haplotypes.)
0
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824
2
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825 Indel realignment::
0
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826
2
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827 -O --dont-left-align-indels
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828 Turn off left-alignment of indels, which is enabled by default.
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829
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830 Input filters::
0
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831
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832 -4 --use-duplicate-reads
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833 Include duplicate-marked alignments in the analysis.
2
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834 default: exclude duplicates marked as such in alignments
0
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835 -m --min-mapping-quality Q
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836 Exclude alignments from analysis if they have a mapping
2
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837 quality less than Q. default: 1
0
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838 -q --min-base-quality Q
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839 Exclude alleles from analysis if their supporting base
2
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840 quality is less than Q. default: 0
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841 -R --min-supporting-allele-qsum Q
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842 Consider any allele in which the sum of qualities of supporting
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843 observations is at least Q. default: 0
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844 -Y --min-supporting-mapping-qsum Q
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845 Consider any allele in which and the sum of mapping qualities of
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846 supporting reads is at least Q. default: 0
0
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847 -Q --mismatch-base-quality-threshold Q
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848 Count mismatches toward --read-mismatch-limit if the base
2
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849 quality of the mismatch is >= Q. default: 10
0
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850 -U --read-mismatch-limit N
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851 Exclude reads with more than N mismatches where each mismatch
2
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852 has base quality >= mismatch-base-quality-threshold.
0
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parents:
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853 default: ~unbounded
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854 -z --read-max-mismatch-fraction N
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parents:
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855 Exclude reads with more than N [0,1] fraction of mismatches where
2
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856 each mismatch has base quality >= mismatch-base-quality-threshold
0
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parents:
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857 default: 1.0
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858 -$ --read-snp-limit N
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parents:
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859 Exclude reads with more than N base mismatches, ignoring gaps
2
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860 with quality >= mismatch-base-quality-threshold.
0
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parents:
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861 default: ~unbounded
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parents:
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862 -e --read-indel-limit N
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parents:
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863 Exclude reads with more than N separate gaps.
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parents:
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864 default: ~unbounded
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865 -0 --standard-filters Use stringent input base and mapping quality filters
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parents:
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866 Equivalent to -m 30 -q 20 -R 0 -S 0
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parents:
diff changeset
867 -F --min-alternate-fraction N
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devteam
parents:
diff changeset
868 Require at least this fraction of observations supporting
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devteam
parents:
diff changeset
869 an alternate allele within a single individual in the
2
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devteam
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diff changeset
870 in order to evaluate the position. default: 0.2
0
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devteam
parents:
diff changeset
871 -C --min-alternate-count N
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devteam
parents:
diff changeset
872 Require at least this count of observations supporting
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devteam
parents:
diff changeset
873 an alternate allele within a single individual in order
2
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
874 to evaluate the position. default: 2
0
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devteam
parents:
diff changeset
875 -3 --min-alternate-qsum N
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devteam
parents:
diff changeset
876 Require at least this sum of quality of observations supporting
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
877 an alternate allele within a single individual in order
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
878 to evaluate the position. default: 0
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devteam
parents:
diff changeset
879 -G --min-alternate-total N
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devteam
parents:
diff changeset
880 Require at least this count of observations supporting
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devteam
parents:
diff changeset
881 an alternate allele within the total population in order
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devteam
parents:
diff changeset
882 to use the allele in analysis. default: 1
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devteam
parents:
diff changeset
883 -! --min-coverage N
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devteam
parents:
diff changeset
884 Require at least this coverage to process a site. default: 0
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devteam
parents:
diff changeset
885
2
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devteam
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diff changeset
886 Population priors::
0
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devteam
parents:
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887
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devteam
parents:
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888 -k --no-population-priors
2
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devteam
parents: 0
diff changeset
889 Equivalent to --pooled-discrete --hwe-priors-off and removal of
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
890 Ewens Sampling Formula component of priors.
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devteam
parents: 0
diff changeset
891
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devteam
parents: 0
diff changeset
892 Mappability priors::
0
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devteam
parents:
diff changeset
893
2
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diff changeset
894 -w --hwe-priors-off
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devteam
parents: 0
diff changeset
895 Disable estimation of the probability of the combination
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diff changeset
896 arising under HWE given the allele frequency as estimated
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897 by observation frequency.
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diff changeset
898 -V --binomial-obs-priors-off
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devteam
parents: 0
diff changeset
899 Disable incorporation of prior expectations about observations.
0
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parents:
diff changeset
900 Uses read placement probability, strand balance probability,
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
901 and read position (5'-3') probability.
2
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parents: 0
diff changeset
902 -a --allele-balance-priors-off
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parents: 0
diff changeset
903 Disable use of aggregate probability of observation balance between alleles
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parents: 0
diff changeset
904 as a component of the priors.
0
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parents:
diff changeset
905
2
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devteam
parents: 0
diff changeset
906 Genotype likelihoods::
0
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parents:
diff changeset
907
2
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parents: 0
diff changeset
908 --observation-bias FILE
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parents: 0
diff changeset
909 Read length-dependent allele observation biases from FILE.
14f952d2a9db Uploaded
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parents: 0
diff changeset
910 The format is [length] [alignment efficiency relative to reference]
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devteam
parents: 0
diff changeset
911 where the efficiency is 1 if there is no relative observation bias.
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diff changeset
912 --base-quality-cap Q
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parents: 0
diff changeset
913 Limit estimated observation quality by capping base quality at Q.
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parents: 0
diff changeset
914 --experimental-gls
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parents: 0
diff changeset
915 Generate genotype likelihoods using 'effective base depth' metric
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diff changeset
916 qual = 1-BaseQual * 1-MapQual. Incorporate partial observations.
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devteam
parents: 0
diff changeset
917 This is the default when contamination estimates are provided.
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parents: 0
diff changeset
918 Optimized for diploid samples.
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parents: 0
diff changeset
919 --prob-contamination F
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parents: 0
diff changeset
920 An estimate of contamination to use for all samples. default: 10e-9
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parents: 0
diff changeset
921 --contamination-estimates FILE
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devteam
parents: 0
diff changeset
922 A file containing per-sample estimates of contamination, such as
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
923 those generated by VerifyBamID. The format should be:
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
924 sample p(read=R|genotype=AR) p(read=A|genotype=AA)
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parents: 0
diff changeset
925 Sample '*' can be used to set default contamination estimates.
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parents: 0
diff changeset
926
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devteam
parents: 0
diff changeset
927 Algorithmic features::
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
928
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devteam
parents: 0
diff changeset
929 --report-genotype-likelihood-max
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devteam
parents: 0
diff changeset
930 Report genotypes using the maximum-likelihood estimate provided
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
931 from genotype likelihoods.
0
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devteam
parents:
diff changeset
932 -B --genotyping-max-iterations N
2
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devteam
parents: 0
diff changeset
933 Iterate no more than N times during genotyping step. default: 1000.
0
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devteam
parents:
diff changeset
934 --genotyping-max-banddepth N
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devteam
parents:
diff changeset
935 Integrate no deeper than the Nth best genotype by likelihood when
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
936 genotyping. default: 6.
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devteam
parents:
diff changeset
937 -W --posterior-integration-limits N,M
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devteam
parents:
diff changeset
938 Integrate all genotype combinations in our posterior space
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devteam
parents:
diff changeset
939 which include no more than N samples with their Mth best
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devteam
parents:
diff changeset
940 data likelihood. default: 1,3.
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devteam
parents:
diff changeset
941 -N --exclude-unobserved-genotypes
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devteam
parents:
diff changeset
942 Skip sample genotypings for which the sample has no supporting reads.
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devteam
parents:
diff changeset
943 -S --genotype-variant-threshold N
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devteam
parents:
diff changeset
944 Limit posterior integration to samples where the second-best
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
945 genotype likelihood is no more than log(N) from the highest
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devteam
parents:
diff changeset
946 genotype likelihood for the sample. default: ~unbounded
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devteam
parents:
diff changeset
947 -j --use-mapping-quality
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devteam
parents:
diff changeset
948 Use mapping quality of alleles when calculating data likelihoods.
2
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devteam
parents: 0
diff changeset
949 -H --harmonic-indel-quality
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devteam
parents: 0
diff changeset
950 Use a weighted sum of base qualities around an indel, scaled by the
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devteam
parents: 0
diff changeset
951 distance from the indel. By default use a minimum BQ in flanking sequence.
0
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devteam
parents:
diff changeset
952 -D --read-dependence-factor N
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devteam
parents:
diff changeset
953 Incorporate non-independence of reads by scaling successive
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devteam
parents:
diff changeset
954 observations by this factor during data likelihood
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devteam
parents:
diff changeset
955 calculations. default: 0.9
2
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parents: 0
diff changeset
956 -= --genotype-qualities
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devteam
parents: 0
diff changeset
957 Calculate the marginal probability of genotypes and report as GQ in
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devteam
parents: 0
diff changeset
958 each sample field in the VCF output.
0
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devteam
parents:
diff changeset
959
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devteam
parents:
diff changeset
960
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devteam
parents:
diff changeset
961 ------
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devteam
parents:
diff changeset
962
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iuc
parents: 5
diff changeset
963 **Acknowledgments**
0
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devteam
parents:
diff changeset
964
2
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devteam
parents: 0
diff changeset
965 The initial version of the wrapper was produced by Dan Blankenberg and upgraded by Anton Nekrutenko.
4
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devteam
parents: 3
diff changeset
966 TNG was developed by Bjoern Gruening
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
967 </help>
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3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
968 <expand macro="citations" />
0
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969 </tool>