Mercurial > repos > iuc > bcftools_filter

annotate bcftools_filter.xml @ 20:5d6653c989cb draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit bfc4ff4956b94885638ae07a2560bac5f84fcca8
author iuc
date Tue, 16 Jul 2024 17:16:52 +0000
parents e7452697afd9
children 46fcafba49ec
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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>Apply fixed-threshold filters</description>
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4 <macros>
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5 <token name="@EXECUTABLE@">filter</token>
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6 <import>macros.xml</import>
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7 </macros>
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e4988fd4d503 "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_FILE@
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14 #set $section = $sec_restrict
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15 @PREPARE_TARGETS_FILE@
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16 @PREPARE_REGIONS_FILE@
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18 bcftools @EXECUTABLE@
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20 ## Filter section
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21 #set $section = $sec_filter
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22 #if $section.SnpGap:
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23 --SnpGap "${section.SnpGap}"
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24 #end if
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25 #if $section.IndelGap:
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26 --IndelGap "${section.IndelGap}"
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27 #end if
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28 #if $section.mode:
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29 #set $mode = str($section.mode).replace(',','')
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30 --mode '$mode'
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31 #end if
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32 #if $section.conditional_soft_filter.selector == 'enabled':
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33 --soft-filter '${section.conditional_soft_filter.soft_filter}'
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34 @MASK@
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35 #end if
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36 #if $section.select_set_GTs:
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37 --set-GTs "${section.select_set_GTs}"
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38 #end if
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39
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40 #set $section = $sec_restrict
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41 @REGIONS@
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42 @TARGETS@
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43 @INCLUDE@
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44 @EXCLUDE@
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45
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46 @OUTPUT_TYPE@
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47 @THREADS@
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48
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49 ## Primary Input/Outputs
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50 @INPUT_FILE@
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51 > '$output_file'
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52 ]]>
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53 </command>
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54 <inputs>
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55 <expand macro="macro_input" />
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56 <section name="sec_restrict" expanded="false" title="Restrict to">
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57 <expand macro="macro_restrict" />
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58 <expand macro="macro_restrict" type="target" label_type="Target" />
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59 <expand macro="macro_include" />
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60 <expand macro="macro_exclude" />
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61 </section>
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62 <section name="sec_filter" expanded="false" title="Filter Options">
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63 <param name="SnpGap" type="integer" label="Snpgap" optional="True" help="(-g) Filter SNPs within &lt;int&gt; base pairs of an indel" />
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64 <param name="IndelGap" type="integer" label="Indelgap" optional="True" help="(-G) Filter clusters of indels separated by &lt;int&gt; or fewer base pairs allowing only one to pass" />
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65 <param name="mode" type="select" label="Mode FILTER annotation" optional="true" multiple="true" display="checkboxes">
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66 <help>(-m)
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67 The default mode replaces existing filters of failed sites with a new FILTER string
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68 while leaving sites which pass untouched when non-empty
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69 and setting to "PASS" when the FILTER string is absent.
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70 </help>
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71 <option value="+">(+) append new FILTER strings of failed sites instead of replacing them</option>
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72 <option value="x">(x) resets filters of sites which pass to "PASS"</option>
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73 </param>
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74 <conditional name="conditional_soft_filter">
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75 <param name="selector" type="select" label="Perform soft filtering">
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76 <option value="disabled">Disabled</option>
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77 <option value="enabled">Enabled</option>
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78 </param>
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79 <when value="disabled"/>
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80 <when value="enabled">
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81 <param argument="--soft-filter" type="text" value="" label="Soft Filter" optional="true">
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82 <help><![CDATA[ (-s)
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83 Annotate FILTER column with STRING or, with +, a unique filter name generated by the program ("Filter%d").
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84 ]]></help>
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85 </param>
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86 <expand macro="macro_restrict" type="mask" label_type="Mask"/>
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87 </when>
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88 </conditional>
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89
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90 <param name="select_set_GTs" type="select" label="Set genotypes of failed samples" optional="true" help="(-S)">
0
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91 <option value=".">to missing (.)</option>
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92 <option value="0">to REF (0)</option>
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93 </param>
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94 </section>
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95 <expand macro="macro_select_output_type" />
061729be105d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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96 </inputs>
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97 <outputs>
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98 <expand macro="macro_vcf_output"/>
061729be105d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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99 </outputs>
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100 <tests>
061729be105d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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101 <test>
061729be105d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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102 <param name="input_file" ftype="vcf" value="filter.1.vcf" />
061729be105d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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103 <param name="mode" value="x" />
061729be105d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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104 <param name="SnpGap" value="2" />
061729be105d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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105 <param name="IndelGap" value="2" />
061729be105d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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106 <param name="output_type" value="v" />
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107 <output name="output_file">
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108 <assert_contents>
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109 <has_text text="PASS" />
061729be105d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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110 <not_has_text text="1006" />
061729be105d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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111 </assert_contents>
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112 </output>
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113 </test>
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114 <test>
061729be105d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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115 <param name="input_file" ftype="vcf" value="filter.2.vcf" />
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116 <param name="exclude" value="QUAL==59.2 || (INDEL=0 &amp; (FMT/GQ=25 | FMT/DP=10))" />
061729be105d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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117 <param name="soft_filter" value="Modified" />
061729be105d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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118 <param name="select_set_GTs" value="." />
061729be105d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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119 <param name="output_type" value="v" />
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120 <output name="output_file">
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121 <assert_contents>
16
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122 <has_text text="genotypes" />
0
061729be105d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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123 <has_text text="AN=2;AC=1" />
16
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124 <has_text_matching expression="TAAAA\tTA,T\t61.5\tPASS" />
0
061729be105d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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125 </assert_contents>
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126 </output>
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127 </test>
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128 <test>
061729be105d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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129 <param name="input_file" ftype="vcf" value="filter.3.vcf" />
7
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130 <param name="exclude" value="INFO/DP=19" />
0
061729be105d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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131 <param name="output_type" value="v" />
061729be105d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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132 <output name="output_file">
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133 <assert_contents>
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iuc
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134 <not_has_text text="3162006" />
061729be105d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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135 <has_text text="3162007" />
061729be105d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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136 </assert_contents>
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137 </output>
061729be105d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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138 </test>
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139
061729be105d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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140 <test>
061729be105d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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141 <param name="input_file" ftype="vcf" value="filter.3.vcf" />
7
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142 <param name="exclude" value="INFO/DP=19" />
16
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143 <section name="sec_filter">
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144 <conditional name="conditional_soft_filter">
e7452697afd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
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145 <param name="selector" value="enabled"/>
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146 <param name="soft_filter" value="XX" />
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147 </conditional>
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148 </section>
0
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149 <param name="output_type" value="v" />
061729be105d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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150 <output name="output_file">
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151 <assert_contents>
061729be105d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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152 <has_text_matching expression="\tXX\tDP=19" />
061729be105d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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153 <has_text_matching expression="\tq20\tAO" />
061729be105d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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154 </assert_contents>
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155 </output>
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156 </test>
061729be105d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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157 <test>
061729be105d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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158 <param name="input_file" ftype="vcf" value="filter.3.vcf" />
7
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diff changeset
159 <param name="exclude" value="INFO/DP=19" />
16
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diff changeset
160 <section name="sec_filter">
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diff changeset
161 <conditional name="conditional_soft_filter">
e7452697afd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
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162 <param name="selector" value="enabled"/>
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163 <param name="soft_filter" value="XX" />
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164 <param name="mode" value="+" />
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165 </conditional>
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166 </section>
0
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167 <param name="output_type" value="v" />
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168 <output name="output_file">
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169 <assert_contents>
16
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diff changeset
170 <has_text_matching expression="238\tXX\tDP=19" />
0
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171 <has_text_matching expression="\tq20\tAO" />
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172 </assert_contents>
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173 </output>
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174 </test>
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175 <test>
061729be105d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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diff changeset
176 <param name="input_file" ftype="vcf" value="filter.3.vcf" />
7
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parents: 5
diff changeset
177 <param name="exclude" value="INFO/DP=19" />
16
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iuc
parents: 14
diff changeset
178 <section name="sec_filter">
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parents: 14
diff changeset
179 <conditional name="conditional_soft_filter">
e7452697afd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
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diff changeset
180 <param name="selector" value="enabled"/>
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parents: 14
diff changeset
181 <param name="soft_filter" value="XX" />
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iuc
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diff changeset
182 <param name="mode" value="+" />
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183 </conditional>
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diff changeset
184 </section>
0
061729be105d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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185 <param name="output_type" value="v" />
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iuc
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diff changeset
186 <output name="output_file">
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187 <assert_contents>
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188 <has_text_matching expression="\tXX\tDP=19" />
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189 <has_text_matching expression="\tq20\tAO=52101" />
0
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190 </assert_contents>
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191 </output>
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192 </test>
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193 <test>
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194 <param name="input_file" ftype="vcf" value="filter.3.vcf" />
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195 <param name="exclude" value="INFO/DP=19" />
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196 <section name="sec_filter">
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197 <conditional name="conditional_soft_filter">
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198 <param name="selector" value="enabled"/>
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199 <param name="soft_filter" value="XX" />
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200 <param name="mode" value="+" />
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201 </conditional>
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202 </section>
0
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203 <param name="output_type" value="v" />
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204 <output name="output_file">
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205 <assert_contents>
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206 <has_text_matching expression="\t238\tXX\tDP=19" />
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207 <has_text_matching expression="\t238\tq20\tAO" />
0
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208 </assert_contents>
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209 </output>
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210 </test>
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211 <test>
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212 <param name="input_file" ftype="vcf" value="filter.3.vcf" />
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213 <param name="exclude" value="FMT/GT=&quot;0/2&quot;" />
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214 <param name="output_type" value="v" />
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215 <output name="output_file">
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216 <assert_contents>
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217 <not_has_text text="3162006" />
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218 <has_text text="3162007" />
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219 </assert_contents>
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220 </output>
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221 </test>
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222 <test>
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223 <param name="input_file" ftype="vcf" value="filter.2.vcf" />
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224 <param name="include" value="FMT/GT=&quot;0/0&quot; &amp;&amp; AC[*]=2" />
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225 <param name="output_type" value="v" />
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226 <output name="output_file">
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227 <assert_contents>
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228 <has_text text="AN=4;AC=2" />
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229 <not_has_text text="AN=4;AC=0" />
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230 </assert_contents>
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231 </output>
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232 </test>
16
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233 <!-- Test region overlap -->
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234 <test>
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235 <param name="input_file" ftype="vcf" value="filter.2.vcf" />
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236 <param name="include" value="FMT/GT=&quot;0/0&quot; &amp;&amp; AC[*]=2" />
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237 <param name="output_type" value="v" />
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238 <section name="sec_restrict">
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239 <param name="regions_overlap" value="1"/>
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240 </section>
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241 <output name="output_file">
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242 <assert_contents>
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243 <has_text text="AN=4;AC=2" />
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244 <not_has_text text="AN=4;AC=0" />
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245 </assert_contents>
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246 </output>
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247 <assert_command>
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248 <has_text text="--regions-overlap" />
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249 </assert_command>
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250 </test>
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251 <!-- Test mask options-->
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252 <test>
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253 <param name="input_file" ftype="vcf" value="filter.3.vcf" />
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254 <param name="exclude" value="INFO/DP=19" />
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255 <section name="sec_filter">
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256 <param name="mode" value="+,x" />
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257 <conditional name="conditional_soft_filter">
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258 <param name="selector" value="enabled"/>
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259 <param name="soft_filter" value="XX" />
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260 <param name="masks_overlap" value="1"/>
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261 </conditional>
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262 </section>
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263
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264 <param name="output_type" value="v" />
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265 <output name="output_file">
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266 <assert_contents>
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267 <has_text_matching expression="\tq20;XX\tDP=19" />
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268 <has_text_matching expression="\tPASS\tAO" />
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269 </assert_contents>
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270 </output>
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271 <assert_command>
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272 <has_text text="--mask-overlap" />
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273 </assert_command>
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274 </test>
0
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275 </tests>
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276 <help><![CDATA[
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277 =====================================
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278 bcftools @EXECUTABLE@
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279 =====================================
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280
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281 Apply fixed-threshold filters.
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282
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283 @REGIONS_HELP@
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284 @TARGETS_HELP@
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285 @EXPRESSIONS_HELP@
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286
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287
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288 @BCFTOOLS_MANPAGE@#@EXECUTABLE@
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289
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290 @BCFTOOLS_WIKI@
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291 ]]>
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292 </help>
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293 <expand macro="citations" />
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294 </tool>