Mercurial > repos > iuc > bcftools_reheader

annotate bcftools_reheader.xml @ 15:b7be725976b6 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit c45135e52ae5039e09272ac6f504d0ceb574aa70
author iuc
date Sat, 23 Jul 2022 13:51:16 +0000
parents 6993b945aefc
children 79489d5685dd
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
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6ca0d413a76a 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'?>
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2 <tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@">
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3 <description>Modify header of VCF/BCF files, change sample names</description>
6ca0d413a76a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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4 <macros>
6ca0d413a76a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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5 <token name="@EXECUTABLE@">reheader</token>
6ca0d413a76a 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>
6ca0d413a76a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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7 </macros>
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6993b945aefc "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" />
0
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9 <expand macro="requirements" />
6ca0d413a76a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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10 <expand macro="version_command" />
6ca0d413a76a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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11 <command detect_errors="aggressive"><![CDATA[
6ca0d413a76a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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12 @PREPARE_ENV@
6ca0d413a76a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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13 @PREPARE_INPUT_FILE@
6ca0d413a76a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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14 bcftools @EXECUTABLE@
6ca0d413a76a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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16 #set $section = $sec_default
6ca0d413a76a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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18 #if $section.header:
6ca0d413a76a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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19 --header "${section.header}"
6ca0d413a76a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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20 #end if
6ca0d413a76a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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21
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22 #if $section.rename_samples.samples_src == 'history':
6ca0d413a76a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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23 --samples "${section.rename_samples.sample_file}"
6ca0d413a76a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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24 #elif $section.rename_samples.samples_src == 'entry':
6ca0d413a76a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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25 --samples "${entered_sample_file}"
6ca0d413a76a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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26 #end if
6ca0d413a76a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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27
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28 ## Primary Input/Outputs
6ca0d413a76a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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29 @INPUT_FILE@
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30 | bcftools view
6ca0d413a76a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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31 @OUTPUT_TYPE@
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32 > '$output_file'
0
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33 ]]>
6ca0d413a76a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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34 </command>
6ca0d413a76a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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35 <configfiles>
6ca0d413a76a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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36 <configfile name="entered_sample_file"><![CDATA[#slurp
6ca0d413a76a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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37 #if $sec_default.rename_samples.samples_src == 'entry'
6ca0d413a76a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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38 $sec_default.rename_samples.sample_lines.__str__.strip()#slurp
6ca0d413a76a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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39 #end if]]></configfile>
6ca0d413a76a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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40 </configfiles>
6ca0d413a76a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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41
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42 <inputs>
6ca0d413a76a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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43 <expand macro="macro_input" />
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44 <section name="sec_default" expanded="true" title="Default Options">
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45 <param name="header" type="data" format="vcf" label="Header" optional="True" help="New header" />
6ca0d413a76a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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46 <conditional name="rename_samples">
6ca0d413a76a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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47 <param name="samples_src" type="select" label="New Sample names">
6ca0d413a76a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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48 <help><![CDATA[
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49 New sample names, one name per line, in the same order as they appear in the VCF file.
6ca0d413a76a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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50 Alternatively, only samples which need to be renamed can be listed as
6ca0d413a76a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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51 "old_name new_name" pairs separated by whitespaces, each on separate line.
6ca0d413a76a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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52 ]]></help>
6ca0d413a76a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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53 <option value="none">Do not change</option>
6ca0d413a76a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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54 <option value="history">From your history</option>
6ca0d413a76a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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55 <option value="entry">From text input</option>
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56 </param>
6ca0d413a76a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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57 <when value="none"/>
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58 <when value="history">
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59 <param name="sample_file" type="data" format="tabular" label="Samples file"/>
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60 </when>
6ca0d413a76a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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61 <when value="entry">
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62 <param name="sample_lines" type="text" area="True" label="Samples text entry" >
6ca0d413a76a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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63 <validator type="regex" message="Either one name per line, or old new sample names per line">^((\S+(\n\S+))|(\S+[ \t]\S+(\n\S+[ \t]\S+)*))$</validator>
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64 <sanitizer sanitize="False"/>
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65 </param>
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66 </when>
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67 </conditional>
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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_file" ftype="vcf" value="reheader.vcf" />
6ca0d413a76a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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77 <param name="header" ftype="vcf" value="reheader.hdr" />
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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="##fileformat=VCFv4.2" />
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82 <has_text text="AAA0001" />
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83 <not_has_text text="XY00001" />
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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_file" ftype="vcf" value="reheader.vcf" />
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89 <param name="samples_src" value="history" />
6ca0d413a76a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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90 <param name="sample_file" ftype="tabular" value="reheader.samples" />
6ca0d413a76a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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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 <not_has_text text="XY00001" />
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95 <has_text_matching expression="FORMAT\tAAA\tBBB"/>
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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_file" ftype="vcf" value="reheader.vcf" />
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101 <param name="samples_src" value="history" />
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102 <param name="sample_file" ftype="tabular" value="reheader.samples2" />
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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 <not_has_text text="XY00001" />
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107 <has_text_matching expression="FORMAT\tAAA\tBBB"/>
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108 </assert_contents>
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109 </output>
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110 </test>
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111 <!--
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112 <test>
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113 <param name="input_file" ftype="vcf" value="reheader.vcf" />
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114 <param name="samples_src" value="entry" />
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115 <param name="sample_lines" value="AAA\nBBB" />
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116 <param name="output_type" value="v" />
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117 <output name="output_file">
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118 <assert_contents>
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119 <not_has_text text="XY00001" />
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120 <has_text_matching expression="FORMAT\tAAA\tBBB"/>
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121 </assert_contents>
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122 </output>
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123 </test>
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124 <test>
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125 <param name="input_file" ftype="vcf" value="reheader.vcf" />
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126 <param name="samples_src" value="entry" />
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127 <param name="sample_lines" value="XY00002 BBB\nXY00001 AAA" />
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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 <not_has_text text="XY00001" />
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132 <has_text_matching expression="FORMAT\tAAA\tBBB"/>
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133 </assert_contents>
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134 </output>
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135 </test>
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136 -->
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137 </tests>
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138 <help><![CDATA[
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139 =====================================
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140 bcftools @EXECUTABLE@
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141 =====================================
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142
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143 Modify header of VCF/BCF files, change sample names.
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144
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145 @BCFTOOLS_MANPAGE@#@EXECUTABLE@
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146
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147 @BCFTOOLS_WIKI@
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148 ]]>
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149 </help>
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150 <expand macro="citations" />
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151 </tool>