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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit 665be55fed0fde169c24f17dd2867b2257b638d8
author iuc
date Sun, 22 Jan 2023 12:42:30 +0000
parents 117d42db0a30
children
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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'
1
d0a6954d0a0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit 665be55fed0fde169c24f17dd2867b2257b638d8
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10 #if $optional_inputs.ref
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11 ln -s '${optional_inputs.ref}' ref.$optional_inputs.ref.ext &&
0
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12 #end if
1
d0a6954d0a0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit 665be55fed0fde169c24f17dd2867b2257b638d8
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13
0
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14 beagle
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15 gt='${gt}'
1
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16 #if $optional_inputs.ref
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17 ref=ref.$optional_inputs.ref.ext
0
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18 #end if
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19 #if $optional_inputs.map
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20 map='${optional_inputs.map}'
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21 #end if
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22 #if $chrom
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23 chrom='${chrom}'
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24 #end if
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25 #if $optional_inputs.excludesamples
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26 excludesamples='${optional_inputs.excludesamples}'
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27 #end if
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28 #if $optional_inputs.excludemarkers
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29 excludemarkers='${optional_inputs.excludemarkers}'
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30 #end if
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31 ne=$ne
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32 window=$window
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33 overlap=$overlap
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34 #if $seed
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35 seed=$seed
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36 #end if
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37 #if $err
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38 err=$err
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39 #end if
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40 burnin=$phasing_parameters.burnin
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41 iterations=$phasing_parameters.iterations
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42 phase-states=$phasing_parameters.phase_states
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43 impute=$imputation_parameters.impute
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44 imp-states=$imputation_parameters.imp_states
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45 imp-segment=$imputation_parameters.imp_segment
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46 imp-step=$imputation_parameters.imp_step
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47 cluster=$imputation_parameters.cluster
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48 ap=$imputation_parameters.ap
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49 gp=$imputation_parameters.gp
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50 out=$out_prefix
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51 nthreads=\${GALAXY_SLOTS:-1}
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52 && gunzip 'out.vcf.gz'
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53 ]]> </command>
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54 <inputs>
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55 <param argument="gt" type="data" format="vcf" label="VCF file"
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56 help="It specifies a VCF file containing genotypes for the study samples.
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57 Each VCF record must contain a GT (genotype) format field"/>
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58 <section name="optional_inputs" title="Optional input files" expanded="true">
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59 <param argument="ref" type="data" format="vcf,bref3" optional="true" label="Bref3 or VCF file with phased genotypes"
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60 help="Each genotype must have two phased, non-missing alleles. If a VCF file is specified, the
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61 phased allele separator must be used '|'"/>
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62 <param argument="map" type="data" format="txt" optional="true" label="PLINK map file with cM units"
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63 help="Beagle uses linear interpolation to estimate genetic positions between map positions. If
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64 no genetic map is specified, Beagle assumes a constant recombination rate of 1 cM per Mb"/>
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65 <param argument="excludesamples" type="data" format="txt" optional="true" label="Samples to exclude"
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66 help="It specifies a file containing samples (one sample identifier per line) to be excluded
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67 from the analysis" />
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68 <param argument="excludemarkers" type="data" format="txt" optional="true" label="Markers to exclude"
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69 help="It specifies a file containing markers (one marker per line) to be excluded from the
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70 analysis. Each line of the file can be either an identifier from a VCF record’s ID field
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71 or a genomic coordinate in the format: CHROM:POS" />
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72 </section>
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73 <param argument="chrom" type="text" optional="true" label="Specify a chromosome interval"
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74 help="Input format: [chrom]:[start]-[end]. The entire chromosome, the beginning, or the end may be
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75 specified by chrom=[chrom], chrom=[chrom]:-[end], and chrom=[chrom]:[start]-, respectively">
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76 <sanitizer invalid_char="">
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77 <valid initial="string.letters,string.digits">
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78 <add value=":" />
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79 <add value="-" />
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80 </valid>
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81 </sanitizer>
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82 <validator type="regex">[0-9a-zA-Z:-]+</validator>
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83 </param>
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84 <param argument="ne" type="integer" min="0" value="1000000" label="Effective population size"
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85 help="The default value is suitable for a large, outbred population. It is needed to specify an
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86 appropriate effective populations size if you are imputing ungenotyped markers in a small
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87 or inbred population"/>
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88 <param argument="window" type="float" min="0" value="40.0" label="Window length in cM"
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89 help="The window parameter must be at least 1.1 times as large as the overlap parameter.
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90 The window parameter controls the amount of memory required for the analysis"/>
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91 <param argument="overlap" type="float" min="0" value="2.0" label="Window overlap in cM"
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92 help="It specifies the cM length of overlap between adjacent sliding windows"/>
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93 <param argument="err" type="float" min="0" max="1" optional="true"
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94 label="Allele mismatch probability for the hidden Markov model"
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95 help="If no err parameter is specified, the err parameter will be set equal 𝜃/(2(𝜃 + 𝐻))
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96 where 𝜃 = 1/(0.5 + ln 𝐻) and 𝐻 is the number of haplotypes"/>
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97 <param argument="seed" type="integer" value="" optional="true" label="Random seed"
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98 help="A random seed is a number used to initialize a pseudorandom number generator" />
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99 <param name="output_log" type="boolean" checked="false" label="Output a log file"/>
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100 <section name="phasing_parameters" title="Phasing parameters">
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101 <param argument="burnin" type="integer" min="0" value="3" label="Max burnin iterations"
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102 help="It is the maximum number of burnin iterations used to estimate an initial haplotype
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103 frequency model for inferring genotype phase" />
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104 <param argument="iterations" type="integer" min="0" value="12" label="Phasing iterations"
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105 help="It is the number of iterations used to estimate genotype phase. Increasing this
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106 parameter will trade increased computation time for increased phasing accuracy" />
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107 <param argument="phase-states" type="integer" min="0" value="280" label="Model states for phasing"
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108 help="It is the number of model states used to estimate genotype phase" />
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109 </section>
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110 <section name="imputation_parameters" title="Imputation parameters">
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111 <param argument="impute" type="boolean" truevalue="true" falsevalue="false"
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112 checked="true" label="Impute ungenotyped markers"
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113 help="It specifies whether markers that are present in the reference panel but absent in
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114 that target will be imputed. This option has no effect if no reference panel is specified"/>
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115 <param argument="imp-states" type="integer" min="0" value="1600" label="Model states for imputation"
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116 help="It is the number of model states used to impute ungenotyped markers" />
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117 <param argument="imp-segment" type="float" min="0" value="6.0" label="Minimum cM length of haplotype segments"
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118 help="It is the minimum cM length of haplotype segments that will be incorporated in the HMM state
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119 space for a target haplotype." />
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120 <param argument="imp-step" type="float" min="0" value="0.1" label="Length in cM for detecting short IBS segments"
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121 help="It is the length in cM of the step used for detecting short IBS segments" />
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122 <param argument="cluster" type="float" min="0" value="0.005" label="Max cM in a marker cluster"
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123 help="It specifies the maximum cM distance between individual markers that are combined
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124 into an aggregate marker when imputing ungenotyped markers" />
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125 <param argument="ap" type="boolean" truevalue="true" falsevalue="false"
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126 checked="false" label="Include posterior allele probabilities"
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127 help="It specifies whether AP1 and AP2 (allele probability) fields will be included in the output
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128 VCF file when imputing ungenotyped markers" />
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129 <param argument="gp" type="boolean" truevalue="true" falsevalue="false"
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130 checked="false" label="Include posterior genotype probabilities"
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131 help="It specifies whether a GP (genotype probability) format field will be included in the output
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132 VCF file when imputing ungenotyped markers. Genotype probabilities are calculated from allele
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133 probabilities assuming Hardy-Weinberg Equilibrium. Consequently, the alleles in the genotype
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134 with highest genotype probability may occasionally be different than the genotype obtained by
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135 taking the allele with highest probability on each haplotype, which is the genotype reported
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136 in the GT format field" />
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137 </section>
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138 </inputs>
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139 <outputs>
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140 <data name="vcf_file" format="vcf" from_work_dir="out.vcf" label="${tool.name} on ${on_string}: VCF file"/>
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141 <data name="log_file" format="txt" from_work_dir="out.log" label="${tool.name} on ${on_string}: log file">
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142 <filter>output_log</filter>
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143 </data>
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144 </outputs>
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145 <tests>
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146 <!-- Test default values -->
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147 <test expect_num_outputs="2">
1
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148 <param name="gt" value="test.vcf.gz" ftype="vcf"/>
0
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149 <param name="chrom" value="22:100-"/>
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150 <param name="ne" value="1000000"/>
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151 <param name="window" value="40.0"/>
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152 <param name="overlap" value="2.0"/>
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153 <param name="err" value="0.02"/>
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154 <param name="seed" value="1"/>
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155 <param name="output_log" value="true"/>
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156 <section name="phasing_parameters">
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157 <param name="burnin" value="3"/>
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158 <param name="iterations" value="12"/>
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159 <param name="phase_states" value="280"/>
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160 </section>
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161 <output name="vcf_file" file="test_output.vcf" ftype="vcf" lines_diff="3"/>
1
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162 <output name="log_file" file="test_output.log" ftype="txt" lines_diff="16">
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163 <assert_contents>
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164 <has_text text="WARNING" negate="true"/>
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165 </assert_contents>
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166 </output>
0
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167 </test>
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168 <!-- Test plink file-->
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169 <test expect_num_outputs="2">
1
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170 <param name="gt" value="test.vcf.gz" ftype="vcf"/>
0
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171 <param name="ne" value="1000000"/>
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diff changeset
172 <param name="window" value="30.0"/>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
173 <param name="overlap" value="3.0"/>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
174 <param name="output_log" value="true"/>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
175 <section name="optional_inputs">
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
176 <param name="map" value="plink.map"/>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
177 </section>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
178 <section name="phasing_parameters">
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
179 <param name="burnin" value="4"/>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
180 <param name="iterations" value="10"/>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
181 <param name="phase_states" value="250"/>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
182 </section>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
183 <output name="vcf_file" ftype="vcf">
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
184 <assert_contents>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
185 <has_text text='ID=GT,Number=1,Type=String,Description="Genotype"'/>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
186 <has_size value="181272"/>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
187 </assert_contents>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
188 </output>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
189 <output name="log_file" ftype="txt">
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
190 <assert_contents>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
191 <has_text text="Reference markers: 223"/>
1
d0a6954d0a0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit 665be55fed0fde169c24f17dd2867b2257b638d8
iuc
parents: 0
diff changeset
192 <has_size value="1586" delta="100"/>
d0a6954d0a0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit 665be55fed0fde169c24f17dd2867b2257b638d8
iuc
parents: 0
diff changeset
193 <has_text text="WARNING" negate="true"/>
d0a6954d0a0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit 665be55fed0fde169c24f17dd2867b2257b638d8
iuc
parents: 0
diff changeset
194 <has_text_matching expression="beagle.*jar finished"/>
0
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
195 </assert_contents>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
196 </output>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
197 </test>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
198 <!-- Test ref VCF input -->
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
199 <test expect_num_outputs="2">
1
d0a6954d0a0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit 665be55fed0fde169c24f17dd2867b2257b638d8
iuc
parents: 0
diff changeset
200 <param name="gt" value="target.vcf.gz" ftype="vcf"/>
0
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
201 <param name="ne" value="1000000"/>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
202 <param name="window" value="40.0"/>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
203 <param name="overlap" value="2.0"/>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
204 <param name="output_log" value="true"/>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
205 <section name="optional_inputs">
1
d0a6954d0a0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit 665be55fed0fde169c24f17dd2867b2257b638d8
iuc
parents: 0
diff changeset
206 <param name="ref" value="ref.vcf.gz" ftype="vcf"/>
0
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
207 </section>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
208 <section name="imputation_parameters">
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
209 <param name="impute" value="true"/>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
210 <param name="imp_states" value="1600"/>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
211 <param name="imp_segment" value="6.0"/>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
212 <param name="imp_step" value="0.1"/>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
213 <param name="cluster" value="0.005"/>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
214 <param name="ap" value="true"/>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
215 <param name="gp" value="true"/>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
216 </section>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
217 <output name="vcf_file" ftype="vcf">
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
218 <assert_contents>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
219 <has_text text='ID=GT,Number=1,Type=String,Description="Genotype"'/>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
220 <has_size value="18635"/>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
221 </assert_contents>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
222 </output>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
223 <output name="log_file" ftype="txt">
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
224 <assert_contents>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
225 <has_text text="Reference markers: 223"/>
1
d0a6954d0a0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit 665be55fed0fde169c24f17dd2867b2257b638d8
iuc
parents: 0
diff changeset
226 <has_size value="1600" delta="100"/>
d0a6954d0a0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit 665be55fed0fde169c24f17dd2867b2257b638d8
iuc
parents: 0
diff changeset
227 <has_text text="WARNING" negate="true"/>
d0a6954d0a0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit 665be55fed0fde169c24f17dd2867b2257b638d8
iuc
parents: 0
diff changeset
228 <has_text_matching expression="beagle.*jar finished"/>
0
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
229 </assert_contents>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
230 </output>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
231 </test>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
232 <!-- Test ref bref3 input -->
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
233 <test expect_num_outputs="1">
1
d0a6954d0a0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit 665be55fed0fde169c24f17dd2867b2257b638d8
iuc
parents: 0
diff changeset
234 <param name="gt" value="target.vcf.gz" ftype="vcf"/>
0
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
235 <param name="ne" value="1000000"/>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
236 <param name="window" value="40.0"/>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
237 <param name="overlap" value="2.0"/>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
238 <section name="optional_inputs">
1
d0a6954d0a0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit 665be55fed0fde169c24f17dd2867b2257b638d8
iuc
parents: 0
diff changeset
239 <param name="ref" value="ref.bref3" ftype="bref3"/>
0
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
240 </section>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
241 <section name="imputation_parameters">
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
242 <param name="impute" value="true"/>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
243 <param name="imp_states" value="1600"/>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
244 <param name="imp_segment" value="6.0"/>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
245 <param name="imp_step" value="0.1"/>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
246 <param name="cluster" value="0.005"/>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
247 <param name="ap" value="true"/>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
248 <param name="gp" value="true"/>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
249 </section>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
250 <output name="vcf_file" ftype="vcf">
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
251 <assert_contents>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
252 <has_text text='ID=GT,Number=1,Type=String,Description="Genotype"'/>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
253 <has_size value="18635"/>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
254 </assert_contents>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
255 </output>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
256 </test>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
257 </tests>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
258 <help><![CDATA[
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
259 .. class:: infomark
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
260
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
diff changeset
261 **Purpose**
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
parents:
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262
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263 Beagle is a program for phasing and imputing missing genotypes. Sporadic missing
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264 genotypes are imputed during phasing. If a reference panel of phased genotypes is specified
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265 with the ref argument, ungenotyped markers that are present in the reference panel can also
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266 be imputed.
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267
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268 Beagle version 5.2 provides significantly faster genotype phasing than version 5.1.
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269 Recent versions of Beagle do not infer genotypes from genotype likelihood input data, but
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270 Beagle versions 4.0 and 4.1 have this capability.
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271
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272 ----
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273
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274 .. class:: infomark
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275
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276 **HapMap genetic maps**
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277
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278 HapMap genetic maps in PLINK format for GRCh36, GRCh37, and GRCh38 are available
1
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279 in `this links <https://bochet.gcc.biostat.washington.edu/beagle/genetic_maps/>`_
0
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280
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281 ----
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282
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283 .. class:: infomark
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284
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285 **Input files**
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286
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287 Beagle uses `Variant Call Format <http://faculty.washington.edu/browning/beagle/intro-to-vcf.html>`_
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288 (VCF) 4.3 for input and output genotype data. Pseuodoautosomal and non-pseudoautosomal
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289 X-chromosome genotypes must be in separate input files and analysed separately unless male
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290 haploid genotypes are coded as homozygous diploid genotypes.
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291
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292 In the VCF file, if any heterozygote genotype is unphased (with "/" allele separator) in a marker window,
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293 it will consider all heterozygote genotypes to be unphased, regardless of the allele separator used ("|" or "/").
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294 Beagle assumes that an the VCF file has a name ending in ".gz" is compressed with gzip or bgzip,
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295 and that a reference VCF file that has a name ending in “.bref3” is compressed with bref version 3.
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296
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297 ----
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298
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299 .. class:: infomark
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300
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301 **Output files**
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302
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303 There are two output files. The log file gives a summary of the analysis that includes the
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304 Beagle version, the command line arguments, and compute time.
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305
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306 The vcf.gz file is a bgzip-compressed VCF file that contains phased, non-missing
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307 genotypes for all non-reference samples. The output vcf.gz file can be uncompressed with the
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308 unix gunzip utility.
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309
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310 If a reference panel is specified and ungenotyped markers are imputed, the VCF INFO
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311 field will contain:
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312
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313 ::
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314
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315 - A "DR2" subfield with the estimated squared correlation between the estimated allele dose and the true allele dose.
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316 - An "AF" subfield with the estimated alternate allele frequencies in the target samples.
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317 - The "IMP" flag if the marker is imputed.
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318
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319 ]]> </help>
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320 <expand macro="citations" />
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321 </tool>