Mercurial > repos > iuc > bcftools_filter

annotate bcftools_filter.xml @ 25:5d8b9dd955c6 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 07:56:38 +0000
parents 0bb5f14a9955
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>Apply fixed-threshold filters</description>
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3 <macros>
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4 <token name="@EXECUTABLE@">filter</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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16 bcftools @EXECUTABLE@
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18 ## Filter section
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19 #set $section = $sec_filter
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20 #if $section.SnpGap:
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21 --SnpGap "${section.SnpGap}"
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22 #end if
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23 #if $section.IndelGap:
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24 --IndelGap "${section.IndelGap}"
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25 #end if
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26 #if $section.mode:
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27 #set $mode = str($section.mode).replace(',','')
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28 --mode '$mode'
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29 #end if
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30 #if $section.conditional_soft_filter.selector == 'enabled':
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31 --soft-filter '${section.conditional_soft_filter.soft_filter}'
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32 @MASK@
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33 #end if
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34 #if $section.select_set_GTs:
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35 --set-GTs "${section.select_set_GTs}"
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36 #end if
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37
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38 #set $section = $sec_restrict
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39 @REGIONS@
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40 @TARGETS@
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41 @INCLUDE@
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42 @EXCLUDE@
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43
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44 @OUTPUT_TYPE@
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45 @THREADS@
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46
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47 ## Primary Input/Outputs
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48 @INPUT_FILE@
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49 > '$output_file'
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50 ]]>
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51 </command>
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52 <inputs>
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53 <expand macro="macro_input"/>
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54 <section name="sec_restrict" expanded="false" title="Restrict to">
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55 <expand macro="macro_region_restrict"/>
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56 <expand macro="macro_target_restrict"/>
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57 <expand macro="macro_include"/>
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58 <expand macro="macro_exclude"/>
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59 </section>
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60 <section name="sec_filter" expanded="false" title="Filter Options">
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61 <param name="SnpGap" type="integer" label="Snpgap" optional="True" help="(-g) Filter SNPs within &lt;int&gt; base pairs of an indel"/>
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62 <param name="IndelGap" type="integer" label="Indelgap" optional="True" help="(-G) Filter clusters of indels separated by &lt;int&gt; or fewer base pairs allowing only one to pass"/>
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63 <param name="mode" type="select" label="Mode FILTER annotation" optional="true" multiple="true" display="checkboxes">
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64 <help>(-m)
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65 The default mode replaces existing filters of failed sites with a new FILTER string
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66 while leaving sites which pass untouched when non-empty
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67 and setting to "PASS" when the FILTER string is absent.
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68 </help>
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69 <option value="+">(+) append new FILTER strings of failed sites instead of replacing them</option>
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70 <option value="x">(x) resets filters of sites which pass to "PASS"</option>
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71 </param>
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72 <conditional name="conditional_soft_filter">
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73 <param name="selector" type="select" label="Perform soft filtering">
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74 <option value="disabled">Disabled</option>
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75 <option value="enabled">Enabled</option>
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76 </param>
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77 <when value="disabled"/>
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78 <when value="enabled">
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79 <param argument="--soft-filter" type="text" value="" label="Soft Filter" optional="true">
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80 <help><![CDATA[ (-s)
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81 Annotate FILTER column with STRING or, with +, a unique filter name generated by the program ("Filter%d").
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82 ]]></help>
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83 </param>
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84 <expand macro="macro_mask_restrict"/>
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85 </when>
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86 </conditional>
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87 <param name="select_set_GTs" type="select" label="Set genotypes of failed samples" optional="true" help="(-S)">
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88 <option value=".">to missing (.)</option>
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89 <option value="0">to REF (0)</option>
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90 </param>
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91 </section>
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92 <expand macro="macro_select_output_type"/>
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93 </inputs>
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94 <outputs>
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95 <expand macro="macro_vcf_output"/>
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96 </outputs>
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97 <tests>
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98 <test>
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99 <param name="input_file" ftype="vcf" value="filter.1.vcf"/>
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100 <section name="sec_filter">
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101 <param name="mode" value="x"/>
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102 </section>
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103 <section name="sec_filter">
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104 <param name="SnpGap" value="2"/>
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105 <param name="IndelGap" value="2"/>
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106 </section>
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107 <param name="output_type" value="v"/>
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108 <output name="output_file">
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109 <assert_contents>
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110 <has_text text="PASS"/>
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111 <not_has_text text="1006"/>
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112 </assert_contents>
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113 </output>
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114 </test>
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115 <test>
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116 <param name="input_file" ftype="vcf" value="filter.2.vcf"/>
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117 <section name="sec_restrict">
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118 <param name="exclude" value="QUAL==59.2 || (INDEL=0 &amp; (FMT/GQ=25 | FMT/DP=10))"/>
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119 </section>
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120 <section name="sec_filter">
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121 <param name="mode" value="+"/>
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122 <conditional name="conditional_soft_filter">
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123 <param name="selector" value="enabled"/>
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124 <param name="soft_filter" value="Modified"/>
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125 </conditional>
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126 <param name="select_set_GTs" value="."/>
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127 </section>
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128 <param name="output_type" value="v"/>
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129 <output name="output_file">
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130 <assert_contents>
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131 <has_text text="genotypes"/>
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132 <has_text text="AN=2;AC=1"/>
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133 <has_text_matching expression="TAAAA\s.*TA,T\s.*61.5\s.*Modified.+"/>
0
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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="filter.3.vcf"/>
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139 <section name="sec_restrict">
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140 <param name="exclude" value="INFO/DP=19"/>
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141 </section>
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142 <param name="output_type" value="v"/>
0
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143 <output name="output_file">
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144 <assert_contents>
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145 <not_has_text text="3162006"/>
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146 <has_text text="3162007"/>
0
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147 </assert_contents>
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148 </output>
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149 </test>
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150 <test>
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151 <param name="input_file" ftype="vcf" value="filter.3.vcf"/>
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152 <section name="sec_restrict">
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153 <param name="exclude" value="INFO/DP=19"/>
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154 </section>
18
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155 <section name="sec_filter">
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156 <conditional name="conditional_soft_filter">
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157 <param name="selector" value="enabled"/>
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158 <param name="soft_filter" value="XX"/>
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159 </conditional>
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160 </section>
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161 <param name="output_type" value="v"/>
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162 <output name="output_file">
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163 <assert_contents>
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164 <has_text_matching expression="\t238\tXX\tDP=19.+"/>
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165 <has_text_matching expression="\tq20\tAO.+"/>
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166 </assert_contents>
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167 </output>
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168 </test>
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169 <test>
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170 <param name="input_file" ftype="vcf" value="filter.3.vcf"/>
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171 <section name="sec_restrict">
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172 <param name="exclude" value="INFO/DP=19"/>
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173 </section>
18
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174 <section name="sec_filter">
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175 <param name="mode" value="+"/>
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176 <conditional name="conditional_soft_filter">
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177 <param name="selector" value="enabled"/>
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178 <param name="soft_filter" value="XX"/>
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179 </conditional>
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180 </section>
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181 <param name="output_type" value="v"/>
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182 <output name="output_file">
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183 <assert_contents>
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184 <has_text_matching expression="238\tq20;XX\tDP=19"/>
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185 <has_text_matching expression="\tq20\tAO"/>
0
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186 </assert_contents>
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187 </output>
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188 </test>
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189 <test>
25
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190 <param name="input_file" ftype="vcf" value="filter.3.vcf"/>
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191 <section name="sec_restrict">
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192 <param name="exclude" value="INFO/DP=19"/>
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193 </section>
18
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194 <section name="sec_filter">
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195 <param name="mode" value="+"/>
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196 <conditional name="conditional_soft_filter">
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197 <param name="selector" value="enabled"/>
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198 <param name="soft_filter" value="XX"/>
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199 </conditional>
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200 </section>
25
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201 <param name="output_type" value="v"/>
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202 <output name="output_file">
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203 <assert_contents>
25
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204 <has_text_matching expression="\tq20;XX\tDP=19"/>
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205 <has_text_matching expression="\tq20\tAO=52101"/>
0
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206 </assert_contents>
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207 </output>
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208 </test>
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209 <test>
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210 <param name="input_file" ftype="vcf" value="filter.3.vcf"/>
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211 <section name="sec_restrict">
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212 <param name="exclude" value="INFO/DP=19"/>
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213 </section>
18
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214 <section name="sec_filter">
25
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215 <param name="mode" value="+"/>
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216 <conditional name="conditional_soft_filter">
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217 <param name="selector" value="enabled"/>
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218 <param name="soft_filter" value="XX"/>
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219 </conditional>
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220 </section>
25
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221 <param name="output_type" value="v"/>
0
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222 <output name="output_file">
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223 <assert_contents>
25
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224 <has_text_matching expression="\t238\tq20;XX\tDP=19"/>
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225 <has_text_matching expression="\t238\tq20\tAO"/>
0
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226 </assert_contents>
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227 </output>
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228 </test>
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229 <test>
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230 <param name="input_file" ftype="vcf" value="filter.3.vcf"/>
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231 <section name="sec_restrict">
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232 <param name="exclude" value="FMT/GT=&quot;0/2&quot;"/>
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233 </section>
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234 <param name="output_type" value="v"/>
0
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235 <output name="output_file">
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236 <assert_contents>
25
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237 <not_has_text text="3162006"/>
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238 <has_text text="3162007"/>
0
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239 </assert_contents>
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240 </output>
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241 </test>
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242 <test>
25
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243 <param name="input_file" ftype="vcf" value="filter.2.vcf"/>
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244 <section name="sec_restrict">
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245 <param name="include" value="FMT/GT=&quot;0/0&quot; &amp;&amp; AC[*]=2"/>
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246 </section>
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247 <param name="output_type" value="v"/>
0
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248 <output name="output_file">
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249 <assert_contents>
25
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250 <has_text text="AN=4;AC=2"/>
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251 <not_has_text text="AN=4;AC=0"/>
0
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252 </assert_contents>
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253 </output>
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254 </test>
18
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255 <!-- Test region overlap -->
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256 <test>
25
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257 <param name="input_file" ftype="vcf" value="filter.2.vcf"/>
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258 <section name="sec_restrict">
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259 <param name="include" value="FMT/GT=&quot;0/0&quot; &amp;&amp; AC[*]=2"/>
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260 </section>
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261 <param name="output_type" value="v"/>
18
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262 <section name="sec_restrict">
25
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263 <conditional name="regions">
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264 <param name="regions_src" value="regions" />
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265 <repeat name="region_specs">
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266 <param name="chrom" value="1" />
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267 </repeat>
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268 </conditional>
18
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269 </section>
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270 <output name="output_file">
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271 <assert_contents>
25
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272 <has_text text="AN=4;AC=2"/>
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273 <not_has_text text="AN=4;AC=0"/>
18
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274 </assert_contents>
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275 </output>
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276 <assert_command>
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277 <has_text text="--regions-overlap"/>
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278 </assert_command>
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279 </test>
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280 <!-- Test mask options-->
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281 <test>
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282 <param name="input_file" ftype="vcf" value="filter.3.vcf"/>
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283 <section name="sec_restrict">
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284 <param name="exclude" value="INFO/DP=19"/>
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285 </section>
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286 <section name="sec_filter">
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287 <param name="mode" value="+,x"/>
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288 <conditional name="conditional_soft_filter">
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289 <param name="selector" value="enabled"/>
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290 <param name="soft_filter" value="XX"/>
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291 <conditional name="masks">
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292 <param name="masks_src" value="masks" />
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293 <repeat name="mask_specs">
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294 <param name="chrom" value="1" />
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295 <param name="start" value="1" />
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296 <param name="stop" value="1000" />
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297 </repeat>
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298 <param name="masks_overlap" value="1"/>
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299 </conditional>
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300 </conditional>
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301 </section>
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302 <param name="output_type" value="v"/>
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303 <output name="output_file">
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304 <assert_contents>
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305 <has_text_matching expression="\tq20;XX\tDP=19"/>
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306 <has_text_matching expression="\tPASS\tAO"/>
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307 </assert_contents>
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308 </output>
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309 <assert_command>
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310 <has_text text="--mask-overlap"/>
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311 </assert_command>
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312 </test>
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313 </tests>
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314 <help><![CDATA[
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315 =====================================
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316 bcftools @EXECUTABLE@
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317 =====================================
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318
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319 Apply fixed-threshold filters.
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320
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321 @REGIONS_HELP@
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322 @TARGETS_HELP@
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323 @EXPRESSIONS_HELP@
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324
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325
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326 @BCFTOOLS_MANPAGE@#@EXECUTABLE@
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327
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328 @BCFTOOLS_HOWTOS@
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329 ]]>
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330 </help>
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331 <expand macro="citations"/>
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332 </tool>