Mercurial > repos > iuc > bcftools_plugin_setgt

annotate bcftools_plugin_setgt.xml @ 25:a5669238dbcc 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 07:44:36 +0000
parents 3e44f68c5f79
children
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1 <tool name="bcftools @EXECUTABLE@" id="bcftools_plugin_@PLUGIN_ID@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>plugin Sets genotypes</description>
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3 <macros>
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4 <token name="@EXECUTABLE@">setGT</token>
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5 <token name="@PLUGIN_ID@">setgt</token>
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6 <import>macros.xml</import>
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7 </macros>
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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_INPUT_FILE@
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13 #set $section = $sec_restrict
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14 @PREPARE_TARGETS_FILE@
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15 @PREPARE_REGIONS_FILE@
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16 bcftools plugin @EXECUTABLE@
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18 ## VCF input section
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19 #set $section = $sec_restrict
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20 @REGIONS@
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21 @TARGETS@
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23 @OUTPUT_TYPE@
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24 @THREADS@
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26 ## Primary Input/Outputs
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27 @INPUT_FILE@
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29 ## Plugin section
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30 #set $section = $sec_plugin
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31 --
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32 --target-gt '$section.target_gt'
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33 --new-gt '$section.new_gt'
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34
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35 #set $section = $sec_restrict
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36 @INCLUDE@
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37 @EXCLUDE@
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38 > '$output_file'
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39 ]]>
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40 </command>
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41 <inputs>
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42 <expand macro="macro_input" />
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43 <section name="sec_restrict" title="Restrict to">
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44 <expand macro="macro_region_restrict" />
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45 <expand macro="macro_target_restrict" />
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46 <expand macro="macro_include" />
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47 <expand macro="macro_exclude" />
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48 </section>
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49 <section name="sec_plugin" expanded="true" title="Plugin Options">
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50 <param name="target_gt" type="select" label="Target genotypes to change">
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51 <option value="./.">./. completely missing (. or ./., depending on ploidy)</option>
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52 <option value="./x">./x partially missing (./0 or .|1)</option>
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53 <option value=".">. partially or completely missing</option>
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54 <option value="a">a all genotypes</option>
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55 <option value="b">b heterozygous genotypes failing two-tailed binomial test</option>
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56 <option value="q">q select genotypes using -i/-e options</option>
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57 </param>
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58 <param name="new_gt" type="select" label="New genotypes to set">
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59 <option value=".">. missing (. or ./., keeps ploidy)</option>
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60 <option value="0">0 reference allele (e.g. 0/0 or 0, keeps ploidy)</option>
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61 <option value="c:GT">c:GT custom genotype (e.g. 0/0, 0, 0/1, m/M, overrides ploidy)</option>
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62 <option value="c:./.">c:./. missing genotype with arbitrary ploidy</option>
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63 <option value="M">M major allele</option>
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64 <option value="m">m minor (the second most common) allele (e.g. 1/1 or 1, keeps ploidy)</option>
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65 <option value="p">p phased genotype</option>
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66 <option value="u">u unphase genotype and sort by allele (1|0 becomes 0/1)</option>
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67 </param>
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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="plugin1.vcf" />
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77 <section name="sec_plugin">
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78 <param name="target_gt" value="." />
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79 <param name="new_gt" value="0" />
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80 </section>
0
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81 <param name="output_type" value="v" />
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82 <output name="output_file">
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83 <assert_contents>
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84 <has_text text="0/0:245" />
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85 </assert_contents>
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86 </output>
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87 </test>
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88 <test>
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89 <param name="input_file" ftype="vcf" value="plugin1.vcf" />
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90 <section name="sec_restrict">
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91 <param name="exclude" value="FMT/GQ>20"/>
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92 </section>
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93 <section name="sec_plugin">
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94 <param name="target_gt" value="q" />
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95 <param name="new_gt" value="." />
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96 </section>
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97 <param name="output_type" value="v" />
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98 <output name="output_file">
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99 <assert_contents>
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100 <has_text text="DP4=1,2,3,4;INDEL;STR=test" />
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101 <has_n_lines n="38"/>
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102 </assert_contents>
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103 </output>
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104 </test>
25
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105 <test>
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106 <param name="input_file" ftype="vcf" value="plugin1.vcf" />
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107 <section name="sec_plugin">
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108 <param name="target_gt" value="." />
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109 <param name="new_gt" value="c:./." />
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110 </section>
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111 <param name="output_type" value="v" />
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112 <output name="output_file">
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113 <assert_contents>
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114 <has_text text="GT" />
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115 <has_text text="DP4=1,2,3,4;INDEL;STR=test" />
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116 </assert_contents>
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117 </output>
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118 </test>
0
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119 </tests>
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120 <help><![CDATA[
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121 =====================================
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122 bcftools @EXECUTABLE@ plugin
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123 =====================================
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124
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125 @REGIONS_HELP@
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126 @TARGETS_HELP@
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127 @EXPRESSIONS_HELP@
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128
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129 ]]></help>
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130 <expand macro="citations" />
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131 </tool>