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annotate beagle.xml @ 0:553b27c30eb8 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
author iuc
date Sat, 03 Jul 2021 23:33:37 +0000
parents
children f75bf16ac901
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0
553b27c30eb8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
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1 <tool id='beagle' name='Beagle' version='@TOOL_VERSION@+galaxy@SUFFIX_VERSION@' profile='20.01'>
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2 <description>phasing genotypes and imputing ungenotyped markers</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro='edam_ontology' />
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7 <expand macro='requirements' />
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8 <command detect_errors='exit_code'><![CDATA[
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9 #set out_prefix='out'
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10 #if $optional_inputs.ref.ext == 'bref3'
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11 ln -s '${optional_inputs.ref}' ref.bref3 &&
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12 #end if
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13 beagle
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14 gt='${gt}'
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15 #if $optional_inputs.ref and $optional_inputs.ref.ext == 'bref3'
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16 ref=ref.bref3
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17 #else if $optional_inputs.ref
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18 ref='${optional_inputs.ref}'
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19 #end if
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20 #if $optional_inputs.map
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21 map='${optional_inputs.map}'
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22 #end if
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23 #if $chrom
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24 chrom='${chrom}'
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25 #end if
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26 #if $optional_inputs.excludesamples
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27 excludesamples='${optional_inputs.excludesamples}'
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28 #end if
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29 #if $optional_inputs.excludemarkers
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30 excludemarkers='${optional_inputs.excludemarkers}'
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31 #end if
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32 ne=$ne
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33 window=$window
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34 overlap=$overlap
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35 #if $seed
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36 seed=$seed
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37 #end if
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38 #if $err
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39 err=$err
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40 #end if
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41 burnin=$phasing_parameters.burnin
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42 iterations=$phasing_parameters.iterations
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43 phase-states=$phasing_parameters.phase_states
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44 impute=$imputation_parameters.impute
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45 imp-states=$imputation_parameters.imp_states
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46 imp-segment=$imputation_parameters.imp_segment
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47 imp-step=$imputation_parameters.imp_step
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48 cluster=$imputation_parameters.cluster
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49 ap=$imputation_parameters.ap
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50 gp=$imputation_parameters.gp
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51 out=$out_prefix
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52 nthreads=\${GALAXY_SLOTS:-1}
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53 && gunzip 'out.vcf.gz'
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54 ]]> </command>
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55 <inputs>
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56 <param argument="gt" type="data" format="vcf" label="VCF file"
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57 help="It specifies a VCF file containing genotypes for the study samples.
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58 Each VCF record must contain a GT (genotype) format field"/>
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59 <section name="optional_inputs" title="Optional input files" expanded="true">
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60 <param argument="ref" type="data" format="vcf,bref3" optional="true" label="Bref3 or VCF file with phased genotypes"
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61 help="Each genotype must have two phased, non-missing alleles. If a VCF file is specified, the
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62 phased allele separator must be used '|'"/>
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63 <param argument="map" type="data" format="txt" optional="true" label="PLINK map file with cM units"
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64 help="Beagle uses linear interpolation to estimate genetic positions between map positions. If
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65 no genetic map is specified, Beagle assumes a constant recombination rate of 1 cM per Mb"/>
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66 <param argument="excludesamples" type="data" format="txt" optional="true" label="Samples to exclude"
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67 help="It specifies a file containing samples (one sample identifier per line) to be excluded
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68 from the analysis" />
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69 <param argument="excludemarkers" type="data" format="txt" optional="true" label="Markers to exclude"
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70 help="It specifies a file containing markers (one marker per line) to be excluded from the
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71 analysis. Each line of the file can be either an identifier from a VCF record’s ID field
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72 or a genomic coordinate in the format: CHROM:POS" />
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73 </section>
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74 <param argument="chrom" type="text" optional="true" label="Specify a chromosome interval"
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75 help="Input format: [chrom]:[start]-[end]. The entire chromosome, the beginning, or the end may be
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76 specified by chrom=[chrom], chrom=[chrom]:-[end], and chrom=[chrom]:[start]-, respectively">
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77 <sanitizer invalid_char="">
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78 <valid initial="string.letters,string.digits">
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79 <add value=":" />
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80 <add value="-" />
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81 </valid>
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82 </sanitizer>
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83 <validator type="regex">[0-9a-zA-Z:-]+</validator>
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84 </param>
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85 <param argument="ne" type="integer" min="0" value="1000000" label="Effective population size"
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86 help="The default value is suitable for a large, outbred population. It is needed to specify an
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87 appropriate effective populations size if you are imputing ungenotyped markers in a small
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88 or inbred population"/>
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89 <param argument="window" type="float" min="0" value="40.0" label="Window length in cM"
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90 help="The window parameter must be at least 1.1 times as large as the overlap parameter.
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91 The window parameter controls the amount of memory required for the analysis"/>
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92 <param argument="overlap" type="float" min="0" value="2.0" label="Window overlap in cM"
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93 help="It specifies the cM length of overlap between adjacent sliding windows"/>
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94 <param argument="err" type="float" min="0" max="1" optional="true"
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95 label="Allele mismatch probability for the hidden Markov model"
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96 help="If no err parameter is specified, the err parameter will be set equal 𝜃/(2(𝜃 + 𝐻))
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97 where 𝜃 = 1/(0.5 + ln 𝐻) and 𝐻 is the number of haplotypes"/>
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98 <param argument="seed" type="integer" value="" optional="true" label="Random seed"
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99 help="A random seed is a number used to initialize a pseudorandom number generator" />
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100 <param name="output_log" type="boolean" checked="false" label="Output a log file"/>
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101 <section name="phasing_parameters" title="Phasing parameters">
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102 <param argument="burnin" type="integer" min="0" value="3" label="Max burnin iterations"
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103 help="It is the maximum number of burnin iterations used to estimate an initial haplotype
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104 frequency model for inferring genotype phase" />
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105 <param argument="iterations" type="integer" min="0" value="12" label="Phasing iterations"
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106 help="It is the number of iterations used to estimate genotype phase. Increasing this
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107 parameter will trade increased computation time for increased phasing accuracy" />
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108 <param argument="phase-states" type="integer" min="0" value="280" label="Model states for phasing"
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109 help="It is the number of model states used to estimate genotype phase" />
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110 </section>
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111 <section name="imputation_parameters" title="Imputation parameters">
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112 <param argument="impute" type="boolean" truevalue="true" falsevalue="false"
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113 checked="true" label="Impute ungenotyped markers"
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114 help="It specifies whether markers that are present in the reference panel but absent in
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115 that target will be imputed. This option has no effect if no reference panel is specified"/>
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116 <param argument="imp-states" type="integer" min="0" value="1600" label="Model states for imputation"
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117 help="It is the number of model states used to impute ungenotyped markers" />
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118 <param argument="imp-segment" type="float" min="0" value="6.0" label="Minimum cM length of haplotype segments"
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119 help="It is the minimum cM length of haplotype segments that will be incorporated in the HMM state
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120 space for a target haplotype." />
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121 <param argument="imp-step" type="float" min="0" value="0.1" label="Length in cM for detecting short IBS segments"
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122 help="It is the length in cM of the step used for detecting short IBS segments" />
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123 <param argument="cluster" type="float" min="0" value="0.005" label="Max cM in a marker cluster"
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124 help="It specifies the maximum cM distance between individual markers that are combined
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125 into an aggregate marker when imputing ungenotyped markers" />
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126 <param argument="ap" type="boolean" truevalue="true" falsevalue="false"
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127 checked="false" label="Include posterior allele probabilities"
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128 help="It specifies whether AP1 and AP2 (allele probability) fields will be included in the output
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129 VCF file when imputing ungenotyped markers" />
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130 <param argument="gp" type="boolean" truevalue="true" falsevalue="false"
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131 checked="false" label="Include posterior genotype probabilities"
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132 help="It specifies whether a GP (genotype probability) format field will be included in the output
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133 VCF file when imputing ungenotyped markers. Genotype probabilities are calculated from allele
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134 probabilities assuming Hardy-Weinberg Equilibrium. Consequently, the alleles in the genotype
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135 with highest genotype probability may occasionally be different than the genotype obtained by
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136 taking the allele with highest probability on each haplotype, which is the genotype reported
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137 in the GT format field" />
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138 </section>
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139 </inputs>
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140 <outputs>
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141 <data name="vcf_file" format="vcf" from_work_dir="out.vcf" label="${tool.name} on ${on_string}: VCF file"/>
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142 <data name="log_file" format="txt" from_work_dir="out.log" label="${tool.name} on ${on_string}: log file">
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143 <filter>output_log</filter>
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144 </data>
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145 </outputs>
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146 <tests>
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147 <!-- Test default values -->
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148 <test expect_num_outputs="2">
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149 <param name="gt" value="test.vcf.gz"/>
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150 <param name="chrom" value="22:100-"/>
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151 <param name="ne" value="1000000"/>
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152 <param name="window" value="40.0"/>
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153 <param name="overlap" value="2.0"/>
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154 <param name="err" value="0.02"/>
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155 <param name="seed" value="1"/>
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156 <param name="output_log" value="true"/>
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157 <section name="phasing_parameters">
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158 <param name="burnin" value="3"/>
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159 <param name="iterations" value="12"/>
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160 <param name="phase_states" value="280"/>
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161 </section>
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162 <output name="vcf_file" file="test_output.vcf" ftype="vcf" lines_diff="3"/>
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163 <output name="log_file" file="test_output.log" ftype="txt" lines_diff="16"/>
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164 </test>
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165 <!-- Test plink file-->
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166 <test expect_num_outputs="2">
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167 <param name="gt" value="test.vcf.gz"/>
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168 <param name="ne" value="1000000"/>
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169 <param name="window" value="30.0"/>
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170 <param name="overlap" value="3.0"/>
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171 <param name="output_log" value="true"/>
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172 <section name="optional_inputs">
553b27c30eb8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
173 <param name="map" value="plink.map"/>
553b27c30eb8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
174 </section>
553b27c30eb8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
175 <section name="phasing_parameters">
553b27c30eb8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
176 <param name="burnin" value="4"/>
553b27c30eb8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
177 <param name="iterations" value="10"/>
553b27c30eb8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
178 <param name="phase_states" value="250"/>
553b27c30eb8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
179 </section>
553b27c30eb8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
180 <output name="vcf_file" ftype="vcf">
553b27c30eb8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
181 <assert_contents>
553b27c30eb8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
182 <has_text text='ID=GT,Number=1,Type=String,Description="Genotype"'/>
553b27c30eb8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
183 <has_size value="181272"/>
553b27c30eb8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
184 </assert_contents>
553b27c30eb8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
185 </output>
553b27c30eb8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
186 <output name="log_file" ftype="txt">
553b27c30eb8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
187 <assert_contents>
553b27c30eb8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
188 <has_text text="Reference markers: 223"/>
553b27c30eb8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
189 <has_size value="1586" delta="10"/>
553b27c30eb8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
190 </assert_contents>
553b27c30eb8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
191 </output>
553b27c30eb8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
192 </test>
553b27c30eb8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
193 <!-- Test ref VCF input -->
553b27c30eb8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
194 <test expect_num_outputs="2">
553b27c30eb8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
195 <param name="gt" value="target.vcf.gz"/>
553b27c30eb8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
196 <param name="ne" value="1000000"/>
553b27c30eb8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
197 <param name="window" value="40.0"/>
553b27c30eb8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
198 <param name="overlap" value="2.0"/>
553b27c30eb8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
199 <param name="output_log" value="true"/>
553b27c30eb8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
200 <section name="optional_inputs">
553b27c30eb8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
201 <param name="ref" value="ref.vcf.gz"/>
553b27c30eb8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
202 </section>
553b27c30eb8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
203 <section name="imputation_parameters">
553b27c30eb8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
204 <param name="impute" value="true"/>
553b27c30eb8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
205 <param name="imp_states" value="1600"/>
553b27c30eb8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
206 <param name="imp_segment" value="6.0"/>
553b27c30eb8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
207 <param name="imp_step" value="0.1"/>
553b27c30eb8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
208 <param name="cluster" value="0.005"/>
553b27c30eb8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
209 <param name="ap" value="true"/>
553b27c30eb8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
210 <param name="gp" value="true"/>
553b27c30eb8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
211 </section>
553b27c30eb8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
212 <output name="vcf_file" ftype="vcf">
553b27c30eb8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
213 <assert_contents>
553b27c30eb8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
214 <has_text text='ID=GT,Number=1,Type=String,Description="Genotype"'/>
553b27c30eb8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
215 <has_size value="18635"/>
553b27c30eb8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
216 </assert_contents>
553b27c30eb8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
217 </output>
553b27c30eb8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
218 <output name="log_file" ftype="txt">
553b27c30eb8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
219 <assert_contents>
553b27c30eb8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
220 <has_text text="Reference markers: 223"/>
553b27c30eb8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
221 <has_size value="1801" delta="10"/>
553b27c30eb8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
222 </assert_contents>
553b27c30eb8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
223 </output>
553b27c30eb8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
224 </test>
553b27c30eb8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
225 <!-- Test ref bref3 input -->
553b27c30eb8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
226 <test expect_num_outputs="1">
553b27c30eb8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
227 <param name="gt" value="target.vcf.gz"/>
553b27c30eb8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
228 <param name="ne" value="1000000"/>
553b27c30eb8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
229 <param name="window" value="40.0"/>
553b27c30eb8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
230 <param name="overlap" value="2.0"/>
553b27c30eb8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
231 <section name="optional_inputs">
553b27c30eb8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
232 <param name="ref" value="ref.bref3"/>
553b27c30eb8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
233 </section>
553b27c30eb8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
234 <section name="imputation_parameters">
553b27c30eb8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
235 <param name="impute" value="true"/>
553b27c30eb8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
236 <param name="imp_states" value="1600"/>
553b27c30eb8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
237 <param name="imp_segment" value="6.0"/>
553b27c30eb8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
238 <param name="imp_step" value="0.1"/>
553b27c30eb8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
239 <param name="cluster" value="0.005"/>
553b27c30eb8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
240 <param name="ap" value="true"/>
553b27c30eb8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
241 <param name="gp" value="true"/>
553b27c30eb8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
242 </section>
553b27c30eb8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
243 <output name="vcf_file" ftype="vcf">
553b27c30eb8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
244 <assert_contents>
553b27c30eb8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
245 <has_text text='ID=GT,Number=1,Type=String,Description="Genotype"'/>
553b27c30eb8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
246 <has_size value="18635"/>
553b27c30eb8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
247 </assert_contents>
553b27c30eb8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
248 </output>
553b27c30eb8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
249 </test>
553b27c30eb8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
250 </tests>
553b27c30eb8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
251 <help><![CDATA[
553b27c30eb8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
252 .. class:: infomark
553b27c30eb8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
253
553b27c30eb8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
254 **Purpose**
553b27c30eb8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
255
553b27c30eb8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
256 Beagle is a program for phasing and imputing missing genotypes. Sporadic missing
553b27c30eb8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
257 genotypes are imputed during phasing. If a reference panel of phased genotypes is specified
553b27c30eb8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
258 with the ref argument, ungenotyped markers that are present in the reference panel can also
553b27c30eb8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
259 be imputed.
553b27c30eb8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
260
553b27c30eb8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
261 Beagle version 5.2 provides significantly faster genotype phasing than version 5.1.
553b27c30eb8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
262 Recent versions of Beagle do not infer genotypes from genotype likelihood input data, but
553b27c30eb8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
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263 Beagle versions 4.0 and 4.1 have this capability.
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264
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265 ----
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266
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267 .. class:: infomark
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268
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269 **HapMap genetic maps**
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270
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271 HapMap genetic maps in PLINK format for GRCh36, GRCh37, and GRCh38 are available
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272 in `this link <http://bochet.gcc.biostat.washington.edu/beagle/genetic_maps/>`_
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273
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274 ----
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275
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276 .. class:: infomark
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277
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278 **Input files**
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279
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280 Beagle uses `Variant Call Format <http://faculty.washington.edu/browning/beagle/intro-to-vcf.html>`_
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281 (VCF) 4.3 for input and output genotype data. Pseuodoautosomal and non-pseudoautosomal
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282 X-chromosome genotypes must be in separate input files and analysed separately unless male
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283 haploid genotypes are coded as homozygous diploid genotypes.
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284
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285 In the VCF file, if any heterozygote genotype is unphased (with "/" allele separator) in a marker window,
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286 it will consider all heterozygote genotypes to be unphased, regardless of the allele separator used ("|" or "/").
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287 Beagle assumes that an the VCF file has a name ending in ".gz" is compressed with gzip or bgzip,
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288 and that a reference VCF file that has a name ending in “.bref3” is compressed with bref version 3.
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289
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290 ----
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291
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292 .. class:: infomark
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293
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294 **Output files**
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295
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296 There are two output files. The log file gives a summary of the analysis that includes the
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297 Beagle version, the command line arguments, and compute time.
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298
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299 The vcf.gz file is a bgzip-compressed VCF file that contains phased, non-missing
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300 genotypes for all non-reference samples. The output vcf.gz file can be uncompressed with the
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301 unix gunzip utility.
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302
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303 If a reference panel is specified and ungenotyped markers are imputed, the VCF INFO
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304 field will contain:
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305
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306 ::
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307
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308 - A "DR2" subfield with the estimated squared correlation between the estimated allele dose and the true allele dose.
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309 - An "AF" subfield with the estimated alternate allele frequencies in the target samples.
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310 - The "IMP" flag if the marker is imputed.
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311
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312 ]]> </help>
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313 <expand macro="citations" />
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314 </tool>