Mercurial > repos > iuc > bcftools_merge

annotate bcftools_merge.xml @ 25:e172f8d4b15a 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 07:41:50 +0000
parents 63f75c284e32
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>Merge multiple VCF/BCF files from non-overlapping sample sets to create one multi-sample file</description>
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3 <macros>
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4 <token name="@EXECUTABLE@">merge</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_FILES@
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12 #set $section = $sec_restrict
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13 @PREPARE_REGIONS_FILE@
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15 bcftools @EXECUTABLE@
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17 ## Header section
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18 #set $section = $sec_header
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19 ${section.print_header}
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20 #if $section.use_header:
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21 --use-header "${section.use_header}"
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22 #end if
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24 ## Merge section
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25 #set $section = $sec_merge
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26 ${section.force_samples}
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28 #if $section.info_rules:
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29 --info-rules "${section.info_rules}"
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30 #end if
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32 #if $section.merge:
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33 --merge "${section.merge}"
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34 $section.no_index
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35 #end if
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37 #set $section = $sec_restrict
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38 @APPLY_FILTERS@
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39 @REGIONS@
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41 @OUTPUT_TYPE@
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42 @THREADS@
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44 ## Primary Input/Outputs
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45 @INPUT_FILES@
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46 > '$output_file'
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47 ]]>
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48 </command>
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49 <inputs>
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50 <expand macro="macro_inputs"/>
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51 <section name="sec_restrict" expanded="false" title="Restrict to">
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52 <expand macro="macro_apply_filters"/>
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53 <expand macro="macro_region_restrict"/>
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54 </section>
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55 <section name="sec_merge" expanded="true" title="Merge Options">
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56 <param name="force_samples" type="boolean" truevalue="--force-samples" falsevalue="" label="Force Samples" help="Resolve duplicate sample names"/>
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57 <param name="info_rules" type="text" label="Info Rules" help="Rules for merging INFO fields (method is one of sum,avg,min,max,join) or &quot;-&quot; to turn off the default [DP:sum,DP4:sum]"/>
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58 <param name="merge" type="select" label="Merge" optional="True" help="Allow multiallelic records for: snps|indels|both|all|none|id, see man page for details [both]">
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59 <option value="none">none - no new multiallelics, output multiple records instead</option>
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60 <option value="snps">snps - allow multiallelic SNP records</option>
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61 <option value="indels">indels - allow multiallelic indel records</option>
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62 <option value="both">both - both SNP and indel records can be multiallelic</option>
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63 <option value="all">all - SNP records can be merged with indel records</option>
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64 <option value="id">id - merge by ID</option>
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65 </param>
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66 <param argument="--no-index" type="boolean" truevalue="--no-index" falsevalue="" checked="false" label="Allow merge unindexed files" help="Requires the input files to have chromosomes in th same order and consistent with the order of sequences in the header"/>
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67 </section>
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68 <section name="sec_header" expanded="false" title="Header Options">
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69 <param name="use_header" type="data" format="vcf" label="Use Header" optional="True" help="Use the provided header"/>
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70 <param name="print_header" type="boolean" truevalue="--print-header" falsevalue="" label="Print Header" help="Print only the merged header and exit"/>
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71 </section>
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72 <expand macro="macro_select_output_type"/>
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73 </inputs>
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74 <outputs>
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75 <expand macro="macro_vcf_output"/>
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76 </outputs>
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77 <tests>
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78 <test>
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79 <param name="input_files" ftype="vcf" value="merge.a.vcf,merge.b.vcf,merge.c.vcf"/>
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80 <section name="sec_merge">
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81 <param name="force_samples" value="true"/>
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82 </section>
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83 <param name="output_type" value="v"/>
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84 <output name="output_file">
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85 <assert_contents>
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86 <has_text text="3000150"/>
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87 <has_text text="3188209"/>
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88 <has_text_matching expression="\tq10;q20\t[\s]*INDEL"/>
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89 </assert_contents>
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90 </output>
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91 </test>
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92 <test>
25
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93 <param name="input_files" ftype="vcf" value="merge.2.a.vcf,merge.2.b.vcf"/>
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94 <section name="sec_merge">
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95 <param name="force_samples" value="true"/>
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96 <param name="merge" value="none"/>
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97 </section>
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98 <param name="output_type" value="v"/>
0
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99 <output name="output_file">
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100 <assert_contents>
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101 <has_text_matching expression="1\t3000000\t.\tC\tCCG\t"/>
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102 <has_text_matching expression="1\t3000000\t.\tC\tG\t"/>
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103 </assert_contents>
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104 </output>
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105 </test>
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106 <test>
25
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107 <param name="input_files" ftype="vcf" value="merge.2.a.vcf,merge.2.b.vcf"/>
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108 <section name="sec_merge">
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109 <param name="force_samples" value="true"/>
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110 <param name="merge" value="both"/>
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111 </section>
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112 <param name="output_type" value="v"/>
0
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113 <output name="output_file">
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114 <assert_contents>
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115 <has_text_matching expression="1\t3000150\t\.\tC\t(A,G|G,A)\t"/>
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116 <has_text_matching expression="1\t3106154\t\.\tC\t(CC,CCC|CCC,CC)\t"/>
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117 </assert_contents>
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118 </output>
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119 </test>
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120 <test>
25
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121 <param name="input_files" ftype="vcf" value="merge.2.a.vcf,merge.2.b.vcf"/>
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122 <section name="sec_merge">
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123 <param name="force_samples" value="true"/>
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124 <param name="merge" value="all"/>
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125 </section>
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126 <param name="output_type" value="v"/>
0
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127 <output name="output_file">
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128 <assert_contents>
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129 <has_text_matching expression="1\t3000000\t\.\tC\t(CCG,G|G,CCG)\t"/>
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130 </assert_contents>
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131 </output>
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132 </test>
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133 <test>
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134 <param name="input_files" ftype="vcf" value="merge.3.a.vcf,merge.3.b.vcf"/>
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135 <section name="sec_merge">
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136 <param name="force_samples" value="true"/>
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137 <param name="info_rules" value="TR:sum,TA:sum,TG:sum"/>
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138 </section>
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139 <param name="output_type" value="v"/>
0
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140 <output name="output_file">
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141 <assert_contents>
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142 <has_text_matching expression="1\t3000000\t.\tC\t(CG,CCG|CCG,CG)\t"/>
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143 <has_text_matching expression="TR=[^;\t]*11"/>
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144 </assert_contents>
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145 </output>
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146 </test>
18
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147 <!-- Test no_index option -->
0
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148 <test>
25
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149 <param name="input_files" ftype="vcf" value="merge.4.a.vcf,merge.4.b.vcf"/>
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150 <section name="sec_merge">
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151 <param name="force_samples" value="true"/>
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152 <param name="merge" value="id"/>
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153 <param name="no_index" value="true"/>
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154 </section>
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155 <param name="output_type" value="v"/>
0
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156 <output name="output_file">
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157 <assert_contents>
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158 <has_text_matching expression="1\t3000000\tid1\tC\t(A,CCG|CCG,A)\t"/>
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159 </assert_contents>
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160 </output>
18
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161 <assert_command>
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162 <has_text text="--no-index"/>
18
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163 </assert_command>
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164 </test>
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165 <!-- Test region overlap option -->
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166 <test>
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167 <param name="input_files" ftype="vcf" value="merge.4.a.vcf,merge.4.b.vcf"/>
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168 <section name="sec_merge">
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169 <param name="force_samples" value="true"/>
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170 <param name="merge" value="id"/>
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171 </section>
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172 <param name="output_type" value="v"/>
18
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173 <section name="sec_restrict">
25
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174 <conditional name="regions">
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175 <param name="regions_src" value="regions" />
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176 <repeat name="region_specs">
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177 <param name="chrom" value="1" />
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178 </repeat>
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179 </conditional>
18
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180 </section>
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181 <output name="output_file">
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182 <assert_contents>
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183 <has_text_matching expression="1\t3000000\tid1\tC\t(A,CCG|CCG,A)\t"/>
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184 </assert_contents>
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185 </output>
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186 <assert_command>
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187 <has_text text="--regions-overlap"/>
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188 </assert_command>
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189 </test>
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190 </tests>
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191 <help><![CDATA[
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192 =====================================
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193 bcftools @EXECUTABLE@
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194 =====================================
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195
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196
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197 Merge multiple VCF/BCF files from non-overlapping sample sets to create one multi-sample file.
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198
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199 Note that only records from different files can be merged, never from the same file.
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200 For "vertical" merge take a look at "bcftools norm" instead.
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201
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202 @REGIONS_HELP@
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203
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204 @BCFTOOLS_MANPAGE@#@EXECUTABLE@
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205
25
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206 @BCFTOOLS_HOWTOS@
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207 ]]>
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208 </help>
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209 <expand macro="citations"/>
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210 </tool>