Mercurial > repos > iuc > bcftools_merge

annotate bcftools_merge.xml @ 16:2215287d5cc9 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
author iuc
date Tue, 20 Sep 2022 13:10:15 +0000
parents 798c063f8fc9
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1 <?xml version='1.0' encoding='utf-8'?>
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2 <tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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3 <description>Merge multiple VCF/BCF files from non-overlapping sample sets to create one multi-sample file</description>
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4 <macros>
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5 <token name="@EXECUTABLE@">merge</token>
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6 <import>macros.xml</import>
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7 </macros>
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798c063f8fc9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit af43d9cf6824f88726900857116f333ff4cdd336"
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8 <expand macro="bio_tools" />
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9 <expand macro="requirements" />
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10 <expand macro="version_command" />
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11 <command detect_errors="aggressive"><![CDATA[
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12 @PREPARE_ENV@
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13 @PREPARE_INPUT_FILES@
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14 #set $section = $sec_restrict
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15 @PREPARE_REGIONS_FILE@
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16
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17 bcftools @EXECUTABLE@
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19 ## Header section
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20 #set $section = $sec_header
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21 ${section.print_header}
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22 #if $section.use_header:
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23 --use-header "${section.use_header}"
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24 #end if
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26 ## Merge section
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27 #set $section = $sec_merge
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28 ${section.force_samples}
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30 #if $section.info_rules:
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31 --info-rules "${section.info_rules}"
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32 #end if
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34 #if $section.merge:
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35 --merge "${section.merge}"
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36 $section.no_index
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37 #end if
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39 #set $section = $sec_restrict
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40 @APPLY_FILTERS@
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41 @REGIONS@
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43 @OUTPUT_TYPE@
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44 @THREADS@
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46 ## Primary Input/Outputs
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47 @INPUT_FILES@
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48 > '$output_file'
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49 ]]>
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50 </command>
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51 <inputs>
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52 <expand macro="macro_inputs" />
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53 <section name="sec_restrict" expanded="false" title="Restrict to">
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54 <expand macro="macro_apply_filters" />
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55 <expand macro="macro_restrict" />
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56 </section>
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57 <section name="sec_merge" expanded="true" title="Merge Options">
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58 <param name="force_samples" type="boolean" truevalue="--force-samples" falsevalue="" label="Force Samples" help="Resolve duplicate sample names" />
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59 <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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60 <param name="merge" type="select" label="Merge" optional="True"
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61 help="Allow multiallelic records for: snps|indels|both|all|none|id, see man page for details [both]" >
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62 <option value="none">none - no new multiallelics, output multiple records instead</option>
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63 <option value="snps">snps - allow multiallelic SNP records</option>
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64 <option value="indels">indels - allow multiallelic indel records</option>
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65 <option value="both">both - both SNP and indel records can be multiallelic</option>
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66 <option value="all">all - SNP records can be merged with indel records</option>
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67 <option value="id">id - merge by ID</option>
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68 </param>
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69 <param argument="--no-index" type="boolean" truevalue="--no-index" falsevalue="" checked="false"
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70 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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71 </section>
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72 <section name="sec_header" expanded="false" title="Header Options">
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73 <param name="use_header" type="data" format="vcf" label="Use Header" optional="True" help="Use the provided header" />
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74 <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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75 </section>
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76 <expand macro="macro_select_output_type" />
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77 </inputs>
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78 <outputs>
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79 <expand macro="macro_vcf_output"/>
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80 </outputs>
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81 <tests>
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82 <test>
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83 <param name="input_files" ftype="vcf" value="merge.a.vcf,merge.b.vcf,merge.c.vcf" />
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84 <param name="force_samples" value="true" />
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85 <param name="output_type" value="v" />
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86 <output name="output_file">
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87 <assert_contents>
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88 <has_text text="3000150" />
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89 <has_text text="3188209" />
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90 <has_text_matching expression="\tq10;q20\t[\s]*INDEL"/>
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91 </assert_contents>
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92 </output>
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93 </test>
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94 <test>
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95 <param name="input_files" ftype="vcf" value="merge.2.a.vcf,merge.2.b.vcf" />
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96 <param name="force_samples" value="true" />
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97 <param name="merge" value="none" />
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98 <param name="output_type" value="v" />
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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>
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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 <param name="force_samples" value="true" />
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109 <param name="merge" value="both" />
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110 <param name="output_type" value="v" />
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111 <output name="output_file">
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112 <assert_contents>
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113 <has_text_matching expression="1\t3000150\t\.\tC\t(A,G|G,A)\t"/>
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114 <has_text_matching expression="1\t3106154\t\.\tC\t(CC,CCC|CCC,CC)\t"/>
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115 </assert_contents>
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116 </output>
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117 </test>
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118 <test>
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119 <param name="input_files" ftype="vcf" value="merge.2.a.vcf,merge.2.b.vcf" />
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120 <param name="force_samples" value="true" />
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121 <param name="merge" value="all" />
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122 <param name="output_type" value="v" />
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123 <output name="output_file">
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124 <assert_contents>
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125 <has_text_matching expression="1\t3000000\t\.\tC\t(CCG,G|G,CCG)\t"/>
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126 </assert_contents>
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127 </output>
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128 </test>
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129 <test>
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130 <param name="input_files" ftype="vcf" value="merge.3.a.vcf,merge.3.b.vcf" />
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131 <param name="force_samples" value="true" />
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132 <param name="info_rules" value="TR:sum,TA:sum,TG:sum" />
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133 <param name="output_type" value="v" />
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134 <output name="output_file">
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135 <assert_contents>
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136 <has_text_matching expression="1\t3000000\t.\tC\t(CG,CCG|CCG,CG)\t"/>
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137 <has_text_matching expression="TR=[^;\t]*11"/>
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138 </assert_contents>
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139 </output>
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140 </test>
16
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141 <!-- Test no_index option -->
0
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142 <test>
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143 <param name="input_files" ftype="vcf" value="merge.4.a.vcf,merge.4.b.vcf" />
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144 <param name="force_samples" value="true" />
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145 <param name="merge" value="id" />
16
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146 <param name="no_index" value="true"/>
0
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147 <param name="output_type" value="v" />
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148 <output name="output_file">
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149 <assert_contents>
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150 <has_text_matching expression="1\t3000000\tid1\tC\t(A,CCG|CCG,A)\t"/>
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151 </assert_contents>
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152 </output>
16
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153 <assert_command>
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154 <has_text text="--no-index" />
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155 </assert_command>
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156 </test>
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157 <!-- Test region overlap option -->
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158 <test>
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159 <param name="input_files" ftype="vcf" value="merge.4.a.vcf,merge.4.b.vcf" />
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160 <param name="force_samples" value="true" />
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161 <param name="merge" value="id" />
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162 <param name="output_type" value="v" />
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163 <section name="sec_restrict">
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164 <param name="regions_overlap" value="1"/>
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165 </section>
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166 <output name="output_file">
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167 <assert_contents>
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168 <has_text_matching expression="1\t3000000\tid1\tC\t(A,CCG|CCG,A)\t"/>
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169 </assert_contents>
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170 </output>
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171 <assert_command>
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172 <has_text text="--regions-overlap" />
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173 </assert_command>
0
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174 </test>
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175 </tests>
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176 <help><![CDATA[
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177 =====================================
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178 bcftools @EXECUTABLE@
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179 =====================================
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180
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181
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182 Merge multiple VCF/BCF files from non-overlapping sample sets to create one multi-sample file.
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183
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184 Note that only records from different files can be merged, never from the same file.
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185 For "vertical" merge take a look at "bcftools norm" instead.
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186
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187 @REGIONS_HELP@
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188
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189 @BCFTOOLS_MANPAGE@#@EXECUTABLE@
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190
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191 @BCFTOOLS_WIKI@
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192 ]]>
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193 </help>
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194 <expand macro="citations" />
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195 </tool>