Mercurial > repos > iuc > bcftools_roh

annotate bcftools_roh.xml @ 25:a85677f5a2ab draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
author iuc
date Tue, 02 Dec 2025 07:53:42 +0000
parents 39cac1b56d93
children
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1 <tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>HMM model for detecting runs of homo/autozygosity</description>
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3 <macros>
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4 <token name="@EXECUTABLE@">roh</token>
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5 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="bio_tools" />
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8 <expand macro="requirements" />
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9 <expand macro="version_command" />
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10 <command detect_errors="aggressive"><![CDATA[
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11 @PREPARE_INPUT_FILE@
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12 #set $section = $sec_restrict
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13 @PREPARE_TARGETS_FILE@
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14 @PREPARE_REGIONS_FILE@
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15 ## General section
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16 #set $section = $sec_general
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17 @PREPARE_AF_FILE@
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19 bcftools @EXECUTABLE@
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21 ## General section
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22 #set $section = $sec_general
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23 @SAMPLE@
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24 @AF_FILE@
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25 #if $section.AF_tag:
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26 --AF-tag "${section.AF_tag}"
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27 #end if
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28 #if $section.AF_dflt:
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29 --AF-dflt "${section.AF_dflt}"
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30 #end if
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31 @ESTIMATE_AF@
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32 #if $section.GTs_only:
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33 --GTs-only "${section.GTs_only}"
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34 #end if
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35 ${section.skip_indels}
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36 #if $section.genetic_map:
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37 --genetic-map "${section.genetic_map}"
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38 #end if
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39 #if $section.rec_rate:
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40 --rec-rate "${section.rec_rate}"
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41 #end if
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42 #if $section.buffer_size:
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43 #if $section.buffer_overlap:
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44 --buffer-size "${section.buffer_size},${section.buffer_overlap}"
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45 #else:
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46 --buffer-size "${section.buffer_size}"
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47 #end if
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48 #end if
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49 $section.ignore_homref
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50 $section.include_noalt
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51
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52 ## HMM section
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53 #set $section = $sec_hmm
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54 #if $section.hw_to_az:
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55 --hw-to-az "${section.hw_to_az}"
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56 #end if
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57 #if $section.az_to_hw:
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58 --az-to-hw "${section.az_to_hw}"
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59 #end if
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60 ${section.viterbi_training}
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61
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62 ## General section
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63 #set $section = $sec_restrict
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64 @REGIONS@
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65 @TARGETS@
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66 @SAMPLES@
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67
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68 #if str($output_type) in ('r','s'):
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69 --output-type $output_type
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70 #end if
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71
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72 ## Primary Input/Outputs
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73 @INPUT_FILE@
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74 > '$output_file'
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75 ]]>
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76 </command>
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77 <inputs>
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78 <expand macro="macro_input" />
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79 <section name="sec_restrict" expanded="false" title="Restrict to">
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80 <expand macro="macro_region_restrict" />
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81 <expand macro="macro_target_restrict" />
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82 <expand macro="macro_samples" />
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83 </section>
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84 <section name="sec_general" expanded="true" title="Roh General Options">
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85 <expand macro="macro_sample" />
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86 <param name="AF_tag" type="text" value="" label="AF TAG" optional="True"
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87 help="Use the specified INFO tag TAG as an allele frequency estimate instead of the defaul AC and AN tags. Sites which do not have TAG will be skipped." />
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88 <param name="AF_dflt" type="float" value="" min="0." max="1." label="AF Default" optional="True" help="If AF is not known, use this allele frequency" />
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89 <expand macro="macro_AF_file" />
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90 <expand macro="macro_estimate_AF" />
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91 <param name="GTs_only" type="float" label="Gts Only" optional="True" help="Use GTs, ignore PLs, use &lt;float&gt; for PL of unseen genotypes. Safe value to use is 30 to account for GT errors." />
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92 <param name="skip_indels" type="boolean" truevalue="--skip-indels" falsevalue="" label="Skip Indels" help="Skip indels as their genotypes are enriched for errors" />
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93 <param name="genetic_map" type="data" format="data" label="Genetic Map" optional="True" help="Genetic map in IMPUTE2 format, single file or mask, where string &quot;{CHROM}&quot; is replaced with chromosome name" />
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94 <param name="rec_rate" type="float" label="Rec Rate" optional="True" help="Constant recombination rate per bp" />
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95 <param name="buffer_size" type="integer" label="Sliding Buffer Size" optional="True">
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96 <help>
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97 Use when the entire many-sample file cannot fit into memory.
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98 The number of sites to keep in memory.
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99 If negative, it is interpreted as the maximum memory to use, in MB.
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100 </help>
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101 </param>
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102 <param name="buffer_overlap" type="integer" min="0" label="Sliding Buffer Overlap" optional="True">
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103 <help>
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104 The number of overlapping sites for the sliding buffer. The default overlap is set to roughly 1% of the buffer size.
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105 </help>
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106 </param>
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107 <param argument="--ignore-homref" type="boolean" truevalue="--ignore-homref" falsevalue="" checked="false" label="Ignore homo-ref" help="skip hom-ref genotypes (0/0)" />
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108 <param argument="--include-noalt" type="boolean" truevalue="--include-noalt" falsevalue="" checked="false" label="Include sites with no ALT allele" help="Ignored by default" />
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109 </section>
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110 <section name="sec_hmm" expanded="true" title="HMM Options">
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111 <param name="hw_to_az" type="float" label="Hw To Az" value="6.7e-8" optional="True" help="P(AZ|HW) transition probability from HW (Hardy-Weinberg) to AZ (autozygous) state" />
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112 <param name="az_to_hw" type="float" label="Az To Hw" value="5e-9" optional="True" help="P(HW|AZ) transition probability from AZ to HW state" />
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113 <param name="viterbi_training" type="boolean" truevalue="--viterbi-training" falsevalue="" label="Viterbi Training" help="Perform Viterbi training to estimate transition probabilities" />
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114 </section>
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115 <param name="output_type" type="select" optional="true" label="limit output">
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116 <option value="s">s:per-site</option>
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117 <option value="r">r:regions</option>
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118 </param>
0
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119 </inputs>
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120 <outputs>
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121 <data name="output_file" format="tabular"/>
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122 </outputs>
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123 <tests>
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124 <test>
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125 <param name="input_file" ftype="vcf" value="roh.vcf" />
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126 <section name="sec_general">
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127 <param name="AF_dflt" value="0.4" />
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128 <param name="GTs_only" value="30" />
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129 </section>
0
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130 <output name="output_file">
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131 <assert_contents>
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132 <has_text_matching expression="ST\tsample\t1"/>
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133 <has_text_matching expression="RG\tsample\t1"/>
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134 </assert_contents>
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135 </output>
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136 </test>
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137 <test>
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138 <param name="input_file" ftype="vcf" value="roh.vcf" />
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139 <section name="sec_general">
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140 <param name="AF_dflt" value="0.4" />
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141 <param name="GTs_only" value="30" />
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142 </section>
5
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143 <param name="output_type" value="r" />
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144 <output name="output_file">
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145 <assert_contents>
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146 <not_has_text text="ST"/>
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147 <has_text_matching expression="RG\tsample\t1"/>
0
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148 </assert_contents>
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149 </output>
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150 </test>
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151 <!-- Test ignore homref and include noalt-->
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152 <test>
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153 <param name="input_file" ftype="vcf" value="roh.vcf" />
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154 <section name="sec_general">
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155 <param name="AF_dflt" value="0.4" />
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156 <param name="GTs_only" value="30" />
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157 <param name="ignore_homref" value="true"/>
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158 <param name="include_noalt" value="true"/>
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159 </section>
18
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160 <param name="output_type" value="r" />
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161 <output name="output_file">
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162 <assert_contents>
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163 <not_has_text text="ST"/>
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164 <has_text_matching expression="RG\tsample\t1"/>
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165 </assert_contents>
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166 </output>
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167 <assert_command>
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168 <has_text text="--ignore-homref" />
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169 <has_text text="--include-noalt" />
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170 </assert_command>
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171 </test>
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172 <!-- Test region overlap-->
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173 <test>
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174 <param name="input_file" ftype="vcf" value="roh.vcf" />
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175 <section name="sec_general">
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176 <param name="AF_dflt" value="0.4" />
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177 <param name="GTs_only" value="30" />
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178 </section>
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179 <section name="sec_restrict">
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180 <conditional name="regions">
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181 <param name="regions_src" value="regions" />
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182 <repeat name="region_specs">
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183 <param name="chrom" value="1" />
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184 </repeat>
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185 </conditional>
18
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186 </section>
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187 <output name="output_file">
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188 <assert_contents>
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189 <has_text_matching expression="ST\tsample\t1"/>
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190 <has_text_matching expression="RG\tsample\t1"/>
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191 </assert_contents>
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192 </output>
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193 <assert_command>
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194 <has_text text="--regions-overlap" />
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195 </assert_command>
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196 </test>
0
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197 </tests>
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198 <help><![CDATA[
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199 =====================================
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200 bcftools @EXECUTABLE@
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201 =====================================
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202
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203 HMM model for detecting runs of autozygosity.
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204
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205 @REGIONS_HELP@
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206 @TARGETS_HELP@
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207
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208 @BCFTOOLS_MANPAGE@#@EXECUTABLE@
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209
25
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210 @BCFTOOLS_HOWTOS@
0
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211 ]]>
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212 </help>
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213 <expand macro="citations" />
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214 </tool>