Mercurial > repos > iuc > bcftools_merge

annotate bcftools_merge.xml @ 1:e8eceb3a69a7 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit a9550d87541eda8b909e6aef1ad8cbf9e9e20d06
author iuc
date Wed, 13 Jul 2016 10:57:34 -0400
parents 5add48c63b9a
children df40d7f9737c
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5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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1 <?xml version='1.0' encoding='utf-8'?>
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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2 <tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@VERSION@.0">
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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3 <description>Merge multiple VCF/BCF files from non-overlapping sample sets to create one multi-sample file</description>
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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4 <macros>
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5 <token name="@EXECUTABLE@">merge</token>
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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6 <import>macros.xml</import>
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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7 </macros>
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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8 <expand macro="requirements" />
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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9 <expand macro="version_command" />
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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10 <command detect_errors="aggressive"><![CDATA[
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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11 @PREPARE_ENV@
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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12 @PREPARE_INPUT_FILES@
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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13 bcftools @EXECUTABLE@
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14
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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15 ## Header section
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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16 #set $section = $sec_header
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17 ${section.print_header}
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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18 #if $section.use_header:
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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19 --use-header "${section.use_header}"
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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20 #end if
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21
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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22 ## Merge section
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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23 #set $section = $sec_merge
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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24 ${section.force_samples}
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25
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26 #if $section.info_rules:
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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27 --info-rules "${section.info_rules}"
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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28 #end if
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29
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30 #if $section.merge:
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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31 --merge "${section.merge}"
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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32 #end if
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33
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34 #set $section = $sec_restrict
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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35 @APPLY_FILTERS@
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36 @REGIONS@
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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37
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38 @OUTPUT_TYPE@
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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39 @THREADS@
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40
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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41 ## Primary Input/Outputs
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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42 @INPUT_FILES@
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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43 > "$output_file"
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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44 ]]>
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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45 </command>
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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46 <inputs>
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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47 <expand macro="macro_inputs" />
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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48 <section name="sec_restrict" expanded="false" title="Restrict to">
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49 <expand macro="macro_apply_filters" />
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50 <expand macro="macro_regions" />
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51 </section>
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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52 <section name="sec_merge" expanded="true" title="Merge Options">
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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53 <param name="force_samples" type="boolean" truevalue="--force-samples" falsevalue="" label="Force Samples" help="Resolve duplicate sample names" />
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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54 <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]" />
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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55 <param name="merge" type="select" label="Merge" optional="True"
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56 help="Allow multiallelic records for: snps|indels|both|all|none|id, see man page for details [both]" >
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57 <option value="none">none - no new multiallelics, output multiple records instead</option>
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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58 <option value="snps">snps - allow multiallelic SNP records</option>
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59 <option value="indels">indels - allow multiallelic indel records</option>
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60 <option value="both">both - both SNP and indel records can be multiallelic</option>
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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61 <option value="all">all - SNP records can be merged with indel records</option>
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62 <option value="id">id - merge by ID</option>
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63 </param>
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64 </section>
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65 <section name="sec_header" expanded="false" title="Header Options">
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66 <param name="use_header" type="data" format="vcf" label="Use Header" optional="True" help="Use the provided header" />
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67 <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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68 </section>
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69 <expand macro="macro_select_output_type" />
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70 </inputs>
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71 <outputs>
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72 <expand macro="macro_vcf_output"/>
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73 </outputs>
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74 <tests>
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75 <test>
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76 <param name="input_files" ftype="vcf" value="merge.a.vcf,merge.b.vcf,merge.c.vcf" />
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77 <param name="force_samples" value="true" />
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78 <param name="output_type" value="v" />
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79 <output name="output_file">
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80 <assert_contents>
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81 <has_text text="3000150" />
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82 <has_text text="3188209" />
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83 <has_text_matching expression="\tq10;q20\t[\s]*INDEL"/>
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84 </assert_contents>
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85 </output>
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86 </test>
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87 <test>
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88 <param name="input_files" ftype="vcf" value="merge.2.a.vcf,merge.2.b.vcf" />
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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89 <param name="force_samples" value="true" />
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90 <param name="merge" value="none" />
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91 <param name="output_type" value="v" />
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92 <output name="output_file">
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93 <assert_contents>
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94 <has_text_matching expression="1\t3000000\t.\tC\tCCG\t"/>
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95 <has_text_matching expression="1\t3000000\t.\tC\tG\t"/>
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96 </assert_contents>
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97 </output>
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98 </test>
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99 <test>
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100 <param name="input_files" ftype="vcf" value="merge.2.a.vcf,merge.2.b.vcf" />
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101 <param name="force_samples" value="true" />
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102 <param name="merge" value="both" />
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103 <param name="output_type" value="v" />
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104 <output name="output_file">
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105 <assert_contents>
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106 <has_text_matching expression="1\t3000150\t\.\tC\t(A,G|G,A)\t"/>
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107 <has_text_matching expression="1\t3106154\t\.\tC\t(CC,CCC|CCC,CC)\t"/>
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108 </assert_contents>
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109 </output>
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110 </test>
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111 <test>
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112 <param name="input_files" ftype="vcf" value="merge.2.a.vcf,merge.2.b.vcf" />
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113 <param name="force_samples" value="true" />
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114 <param name="merge" value="all" />
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115 <param name="output_type" value="v" />
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116 <output name="output_file">
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117 <assert_contents>
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118 <has_text_matching expression="1\t3000000\t\.\tC\t(CCG,G|G,CCG)\t"/>
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119 </assert_contents>
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120 </output>
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121 </test>
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122 <test>
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123 <param name="input_files" ftype="vcf" value="merge.3.a.vcf,merge.3.b.vcf" />
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124 <param name="force_samples" value="true" />
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125 <param name="info_rules" value="TR:sum,TA:sum,TG:sum" />
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126 <param name="output_type" value="v" />
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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(CG,CCG|CCG,CG)\t"/>
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130 <has_text_matching expression="TR=[^;\t]*11"/>
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131 </assert_contents>
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132 </output>
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133 </test>
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134 <test>
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135 <param name="input_files" ftype="vcf" value="merge.4.a.vcf,merge.4.b.vcf" />
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136 <param name="force_samples" value="true" />
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137 <param name="merge" value="id" />
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138 <param name="output_type" value="v" />
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139 <output name="output_file">
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140 <assert_contents>
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141 <has_text_matching expression="1\t3000000\tid1\tC\t(A,CCG|CCG,A)\t"/>
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142 </assert_contents>
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143 </output>
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144 </test>
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145 </tests>
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146 <help><![CDATA[
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147 =====================================
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148 bcftools @EXECUTABLE@
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149 =====================================
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150
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151
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152 Merge multiple VCF/BCF files from non-overlapping sample sets to create one multi-sample file.
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153
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154 Note that only records from different files can be merged, never from the same file.
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155 For "vertical" merge take a look at "bcftools norm" instead.
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156
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157 @REGIONS_HELP@
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158
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159 @BCFTOOLS_MANPAGE@#@EXECUTABLE@
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160
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161 @BCFTOOLS_WIKI@
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162 ]]>
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163 </help>
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164 <expand macro="citations" />
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165 </tool>