annotate bcftools_annotate.xml @ 18:ebe5fc018e72 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 087a38fc2eade9f3a286d672ba61571b0b69a797
author iuc
date Mon, 26 Sep 2022 18:14:08 +0000
parents 8a2e296c07ef
children
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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>Annotate and edit VCF/BCF files</description>
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4 <macros>
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5 <token name="@EXECUTABLE@">annotate</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_ENV@
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13 @PREPARE_INPUT_FILE@
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14 #set $annotation_file = None
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15 #set $annotation_hdr = None
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16 #set $section = $sec_annofile
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17 #if $section.annofile.anno_fmt == 'vcf':
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18 #if $section.annofile.annotations.is_of_type('vcf')
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19 #set $annotation_file = 'annotations.vcf.gz'
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20 bgzip -c '$section.annofile.annotations' > $annotation_file &&
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21 bcftools index $annotation_file &&
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22 #elif $section.annofile.annotations.is_of_type('bcf')
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23 #set $annotation_file = 'annotations.bcf'
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24 ln -s '$section.annofile.annotations' $annotation_file &&
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25 #if $section.annofile.annotations.metadata.bcf_index:
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26 ln -s '${section.annofile.annotations.metadata.bcf_index}' ${annotation_file}.csi &&
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27 #else
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28 bcftools index $annotation_file &&
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29 #end if
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30 #end if
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31 #elif $section.annofile.anno_fmt == 'tab':
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32 #if $section.annofile.annotations.is_of_type('bed')
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33 #set $annotation_file = 'annotations.bed.gz'
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34 bgzip -c '$section.annofile.annotations' > $annotation_file &&
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35 tabix -s 1 -b 2 -e 3 $annotation_file &&
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36 #else:
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37 #set $annotation_file = 'annotations.tab.gz'
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38 bgzip -c '$section.annofile.annotations' > $annotation_file &&
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39 tabix -s 1 -b 2 -e 2 $annotation_file &&
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40 #end if
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41 #if $section.annofile.header_file:
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42 #set $annotation_hdr = $section.annofile.header_file
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43 #elif $section.annofile.header_lines:
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44 #set $annotation_hdr = 'annotation.hdr'
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45 grep '^\#\#INFO' '${hdr_file}' > $annotation_hdr &&
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46 #end if
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47 #end if
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48 #set $section = $sec_restrict
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49
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50 bcftools @EXECUTABLE@
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51 @PREPARE_REGIONS_FILE@
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52
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53 #set $section = $sec_annofile
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54 @COLUMNS@
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55 #if $annotation_file:
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56 --annotations '${annotation_file}'
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57 #end if
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58 #if $annotation_hdr:
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59 --header-lines '${annotation_hdr}'
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60 #end if
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61
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62 #if $section.set_id:
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63 --set-id '${section.set_id}'
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64 #end if
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65 #if $section.mark_sites:
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66 --mark-sites '${section.mark_sites}'
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67 #end if
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68 #if $section.min_overlap
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69 --min-overlap '$section.min_overlap'
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70 #end if
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72 #set $section = $sec_annotate
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73 #if $section.rename_chrs:
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74 --rename-chrs '${section.rename_chrs}'
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75 #end if
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76 #if $section.remove:
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77 --remove '${section.remove}'
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78 #end if
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79 #if $section.rename_annots
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80 --rename-annots '$section.rename_annots'
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81 #end if
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82
0
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84 ## Default section
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85 #set $section = $sec_restrict
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86 @INCLUDE@
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87 @EXCLUDE@
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88 @COLLAPSE@
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89 @REGIONS@
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90 @SAMPLES@
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91
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92 @OUTPUT_TYPE@
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93 @THREADS@
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94
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95 ## Primary Input/Outputs
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96 @INPUT_FILE@
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97 > '$output_file'
0
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98 ]]>
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99 </command>
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100 <configfiles>
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101 <configfile name="hdr_file"><![CDATA[#slurp
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102 #if $sec_annofile.annofile.anno_fmt == 'tab' and str($sec_annofile.annofile.header_lines) != '':
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103 $sec_annofile.annofile.header_lines.__str__.strip()#slurp
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104 #end if]]></configfile>
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105 </configfiles>
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106 <inputs>
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107 <expand macro="macro_input" />
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108 <section name="sec_annofile" expanded="false" title="Add Annotations">
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109 <expand macro="macro_columns" />
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110 <conditional name="annofile">
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111 <param name="anno_fmt" type="select" label="Annotations File">
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112 <option value="none">None</option>
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113 <option value="vcf">From a VCF/BCF file</option>
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114 <option value="tab">From a BED or tab-delimited file</option>
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115 </param>
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116 <when value="none"/>
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117 <when value="vcf">
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118 <param name="annotations" type="data" format="vcf,bcf" label="Annotations VCF"/>
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119 </when>
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120 <when value="tab">
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121 <param name="annotations" type="data" format="tabular,bed" label="Annotations">
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122 <help><![CDATA[
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123 BED, or a tab-delimited file with mandatory columns CHROM, POS (or, alternatively, FROM and TO),
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124 optional columns REF and ALT, and arbitrary number of annotation columns.
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125 Note that in case of tab-delimited file, the coordinates POS, FROM and TO are one-based and inclusive.
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126 ]]></help>
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127 </param>
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128 <param name="header_file" type="data" format="txt" label="Header Lines File" optional="true" help="lines which should be appended to the VCF header" />
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129 <param name="header_lines" type="text" area="true" label="Header Lines" optional="true" help="lines which should be appended to the VCF header" >
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130 <help><![CDATA[
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131 ##INFO=<ID=NUMERIC_TAG,Number=1,Type=Integer,Description="Example header line">
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132 ##INFO=<ID=STRING_TAG,Number=1,Type=String,Description="Yet another header line">
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133 ]]></help>
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134 <sanitizer sanitize="False"/>
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135 </param>
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136 </when>
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137 </conditional>
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138 <param argument="--mark-sites" type="text" value="" label="Mark Sites TAG"
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139 help="add INFO/TAG flag to sites which are (&quot;+&quot;) or are not (&quot;-&quot;) listed in the annotations file" />
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140 <param argument="--min-overlap" type="text" value="" label="Minimum required overlap of intersecting regions" optional="true" help="Minimum overlap required as a fraction of the variant in the annotation -a file (ANN), in the target VCF file (:VCF), or both for reciprocal overlap (ANN:VCF). By default overlaps of arbitrary length are sufficient.">
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141 <sanitizer invalid_char="">
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142 <valid initial="string.digits">
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143 <add value=":" />
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144 <add value="." />
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145 </valid>
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146 </sanitizer>
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147 <validator type="regex">[0-9.:]+</validator>
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148 </param>
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149 <param argument="--set-id" type="text" value="" optional="true" label="Set Id">
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150 <help>Assign ID on the fly using the given format.
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151 By default all existing IDs are replaced.
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152 If the format string is preceded by "+", only missing IDs will be set.
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153 For example: '%CHROM\_%POS\_%REF\_%FIRST_ALT'
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154 </help>
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155 <sanitizer sanitize="False"/>
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156 <validator type="regex" message="">^([+]?(%[A-Z_]+)(\\_%[A-Z_]+)*)?$</validator>
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157 </param>
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158 </section>
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159 <section name="sec_annotate" expanded="false" title="Change Annotations">
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160 <param argument="--remove" type="text" value="" label="Remove annotations" optional="true">
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161 <help><![CDATA[
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162 List of annotations to remove.
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163 Use "FILTER" to remove all filters or "FILTER/SomeFilter" to remove a specific filter.
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164 Similarly, "INFO" can be used to remove all INFO tags and "FORMAT" to remove all FORMAT tags except GT.
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165 To remove all INFO tags except "FOO" and "BAR", use "^INFO/FOO,INFO/BAR" (and similarly for FORMAT and FILTER).
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166 "INFO" can be abbreviated to "INF" and "FORMAT" to "FMT".
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167 ]]></help>
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168 <validator type="regex" message="">^(\^?[A-Z]+(/\w+)?(,\^?[A-Z]+(/\w+)?)*)?$</validator>
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169 </param>
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170 <param argument="--rename-chrs" type="data" format="tabular" label="Rename CHROM" optional="true"
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171 help="rename chromosomes according to the map in file, with old_name new_name pairs separated by whitespaces, each on a separate line." />
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172 <param argument="--rename-annots" type="data" format="tabular" optional="true" label="Rename annotations" help="TYPE/old\tnew, where TYPE is one of FILTER,INFO,FORMAT" />
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173 </section>
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174 <section name="sec_restrict" expanded="false" title="Restrict to">
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175 <expand macro="macro_include" />
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176 <expand macro="macro_exclude" />
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177 <expand macro="macro_collapse" />
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178 <expand macro="macro_restrict" />
0
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iuc
parents:
diff changeset
179 <expand macro="macro_samples" />
e58e34d48868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
180 </section>
e58e34d48868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
181 <expand macro="macro_select_output_type" />
e58e34d48868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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diff changeset
182 </inputs>
e58e34d48868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
183 <outputs>
e58e34d48868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
184 <expand macro="macro_vcf_output"/>
e58e34d48868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
185 </outputs>
e58e34d48868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
186 <tests>
e58e34d48868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
187 <test>
e58e34d48868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
188 <param name="input_file" ftype="vcf" value="annotate.vcf" />
e58e34d48868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
189 <param name="anno_fmt" value="tab" />
e58e34d48868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
190 <param name="annotations" value="annotate.tab" />
e58e34d48868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
191 <param name="header_file" value="annotate.hdr" />
e58e34d48868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
192 <param name="columns" value="CHROM,POS,REF,ALT,ID,QUAL,INFO/T_INT,INFO/T_FLOAT,INDEL" />
e58e34d48868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
193 <param name="output_type" value="v" />
e58e34d48868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
194 <output name="output_file">
e58e34d48868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
195 <assert_contents>
e58e34d48868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
196 <has_text text="snp_3000150" />
e58e34d48868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
197 </assert_contents>
e58e34d48868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
198 </output>
e58e34d48868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
199 </test>
e58e34d48868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
200 <test>
e58e34d48868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
201 <param name="input_file" ftype="vcf" value="annotate.vcf" />
15
2958e3b49ad4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ccc967cdce26379110361f8dea521bade23f8612"
iuc
parents: 14
diff changeset
202 <section name="sec_annofile">
2958e3b49ad4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ccc967cdce26379110361f8dea521bade23f8612"
iuc
parents: 14
diff changeset
203 <param name="columns" value="CHROM,FROM,TO,T_STR" />
2958e3b49ad4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ccc967cdce26379110361f8dea521bade23f8612"
iuc
parents: 14
diff changeset
204 <conditional name="annofile">
2958e3b49ad4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ccc967cdce26379110361f8dea521bade23f8612"
iuc
parents: 14
diff changeset
205 <param name="anno_fmt" value="tab" />
2958e3b49ad4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ccc967cdce26379110361f8dea521bade23f8612"
iuc
parents: 14
diff changeset
206 <param name="annotations" value="annotate2.tab" />
2958e3b49ad4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ccc967cdce26379110361f8dea521bade23f8612"
iuc
parents: 14
diff changeset
207 <param name="header_file" value="annotate.hdr" />
2958e3b49ad4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ccc967cdce26379110361f8dea521bade23f8612"
iuc
parents: 14
diff changeset
208 </conditional>
2958e3b49ad4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ccc967cdce26379110361f8dea521bade23f8612"
iuc
parents: 14
diff changeset
209 <param name="set_id" value="%CHROM\_%POS\_%REF\_%FIRST_ALT" />
2958e3b49ad4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ccc967cdce26379110361f8dea521bade23f8612"
iuc
parents: 14
diff changeset
210 </section>
0
e58e34d48868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
211 <param name="output_type" value="v" />
e58e34d48868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
212 <output name="output_file">
e58e34d48868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
213 <assert_contents>
e58e34d48868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
214 <has_text text="T_STR=region_3000150_3106154" />
15
2958e3b49ad4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ccc967cdce26379110361f8dea521bade23f8612"
iuc
parents: 14
diff changeset
215 <has_text text="1_3062915_GTTT_G" />
0
e58e34d48868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
216 </assert_contents>
e58e34d48868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
217 </output>
e58e34d48868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
218 </test>
e58e34d48868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
219 <test>
e58e34d48868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
220 <param name="input_file" ftype="vcf" value="annotate.vcf" />
e58e34d48868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
221 <param name="anno_fmt" value="vcf" />
e58e34d48868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
222 <param name="annotations" value="annots.vcf" />
e58e34d48868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
223 <param name="columns" value="STR,ID,QUAL,FILTER" />
e58e34d48868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
224 <param name="output_type" value="v" />
e58e34d48868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
225 <output name="output_file">
e58e34d48868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
226 <assert_contents>
e58e34d48868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
227 <has_text text="idIndel" />
e58e34d48868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
228 <has_text text="STR=testSNP" />
e58e34d48868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
229 </assert_contents>
e58e34d48868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
230 </output>
e58e34d48868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
231 </test>
e58e34d48868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
232 <test>
9
a80ec64f9101 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 942ca2971ae6a72e548fde6186c6408a1e236653
iuc
parents: 8
diff changeset
233 <param name="input_file" ftype="vcf" value="annotate.vcf" />
a80ec64f9101 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 942ca2971ae6a72e548fde6186c6408a1e236653
iuc
parents: 8
diff changeset
234 <param name="anno_fmt" value="vcf" />
a80ec64f9101 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 942ca2971ae6a72e548fde6186c6408a1e236653
iuc
parents: 8
diff changeset
235 <param name="annotations" value="annots.bcf" />
a80ec64f9101 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 942ca2971ae6a72e548fde6186c6408a1e236653
iuc
parents: 8
diff changeset
236 <param name="columns" value="STR,ID,QUAL,FILTER" />
a80ec64f9101 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 942ca2971ae6a72e548fde6186c6408a1e236653
iuc
parents: 8
diff changeset
237 <param name="output_type" value="v" />
a80ec64f9101 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 942ca2971ae6a72e548fde6186c6408a1e236653
iuc
parents: 8
diff changeset
238 <output name="output_file">
a80ec64f9101 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 942ca2971ae6a72e548fde6186c6408a1e236653
iuc
parents: 8
diff changeset
239 <assert_contents>
a80ec64f9101 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 942ca2971ae6a72e548fde6186c6408a1e236653
iuc
parents: 8
diff changeset
240 <has_text text="idIndel" />
a80ec64f9101 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 942ca2971ae6a72e548fde6186c6408a1e236653
iuc
parents: 8
diff changeset
241 <has_text text="STR=testSNP" />
a80ec64f9101 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 942ca2971ae6a72e548fde6186c6408a1e236653
iuc
parents: 8
diff changeset
242 </assert_contents>
a80ec64f9101 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 942ca2971ae6a72e548fde6186c6408a1e236653
iuc
parents: 8
diff changeset
243 </output>
a80ec64f9101 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 942ca2971ae6a72e548fde6186c6408a1e236653
iuc
parents: 8
diff changeset
244 </test>
a80ec64f9101 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 942ca2971ae6a72e548fde6186c6408a1e236653
iuc
parents: 8
diff changeset
245 <test>
0
e58e34d48868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
246 <param name="input_file" ftype="vcf" value="annotate2.vcf" />
e58e34d48868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
247 <param name="anno_fmt" value="vcf" />
e58e34d48868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
248 <param name="annotations" value="annots2.vcf" />
e58e34d48868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
249 <param name="columns" value="ID,QUAL,FILTER,INFO,FMT" />
e58e34d48868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
250 <param name="output_type" value="v" />
e58e34d48868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
251 <output name="output_file">
e58e34d48868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
252 <assert_contents>
e58e34d48868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
253 <has_text text="q99" />
e58e34d48868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
254 <has_text text="FLAG;IINT=88,99;IFLT=8.8,9.9;ISTR=888,999" />
e58e34d48868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
255 </assert_contents>
e58e34d48868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
256 </output>
e58e34d48868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
257 </test>
e58e34d48868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
258 <test>
e58e34d48868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
259 <param name="input_file" ftype="vcf" value="annotate2.vcf" />
e58e34d48868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
260 <param name="anno_fmt" value="vcf" />
e58e34d48868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
261 <param name="annotations" value="annots2.vcf" />
e58e34d48868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
262 <param name="columns" value="ID,QUAL,FILTER,INFO,FMT" />
e58e34d48868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
263 <param name="samples" value="A" />
e58e34d48868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
264 <param name="output_type" value="v" />
e58e34d48868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
265 <output name="output_file">
e58e34d48868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
266 <assert_contents>
e58e34d48868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
267 <has_text text="q11" />
e58e34d48868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
268 <has_text text="FLAG;IINT=88,99;IFLT=8.8,9.9;ISTR=888,999" />
e58e34d48868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
269 </assert_contents>
e58e34d48868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
270 </output>
e58e34d48868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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271 </test>
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272 <test>
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273 <param name="input_file" ftype="vcf" value="annotate3.vcf" />
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274 <param name="anno_fmt" value="none" />
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275 <param name="remove" value="ID,QUAL,^FILTER/fltA,FILTER/fltB,^INFO/AA,INFO/BB,^FMT/GT,FMT/PL" />
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276 <param name="output_type" value="v" />
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277 <output name="output_file">
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278 <assert_contents>
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279 <not_has_text text="fltY" />
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280 </assert_contents>
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281 </output>
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282 </test>
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283 <test>
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284 <param name="input_file" ftype="vcf" value="annotate3.vcf" />
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285 <param name="anno_fmt" value="none" />
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286 <param name="remove" value="FORMAT" />
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287 <param name="output_type" value="v" />
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288 <output name="output_file">
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289 <assert_contents>
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290 <not_has_text text="GT:X:PL:Y:AA" />
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291 </assert_contents>
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292 </output>
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293 </test>
17
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294 <!-- Test region overlap option -->
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295 <test>
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296 <param name="input_file" ftype="vcf" value="annotate3.vcf" />
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297 <param name="anno_fmt" value="none" />
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298 <param name="remove" value="FORMAT" />
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299 <param name="output_type" value="v" />
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300 <section name="sec_restrict">
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301 <param name="regions_overlap" value="1"/>
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302 </section>
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303 <output name="output_file">
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304 <assert_contents>
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305 <not_has_text text="GT:X:PL:Y:AA" />
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306 </assert_contents>
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307 </output>
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308 <assert_command>
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309 <has_text text="--regions-overlap" />
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310 </assert_command>
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311 </test>
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312 <!-- Test min overlap option -->
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313 <test>
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314 <param name="input_file" ftype="vcf" value="annotate3.vcf" />
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315 <param name="anno_fmt" value="none" />
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316 <param name="remove" value="FORMAT" />
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317 <param name="output_type" value="v" />
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318 <section name="sec_annofile">
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319 <param name="min_overlap" value="0.5"/>
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320 </section>
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321 <output name="output_file">
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322 <assert_contents>
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323 <not_has_text text="GT:X:PL:Y:AA" />
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324 </assert_contents>
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325 </output>
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326 <assert_command>
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327 <has_text text="--min-overlap" />
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328 </assert_command>
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329 </test>
0
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330 </tests>
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331 <help><![CDATA[
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332 ==================================
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333 bcftools @EXECUTABLE@
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334 ==================================
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335
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336 Annotate and edit VCF/BCF files.
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337
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338 Examples:
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339
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340 # Remove three fields
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341 bcftools annotate -x ID,INFO/DP,FORMAT/DP file.vcf.gz
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342
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343 # Remove all INFO fields and all FORMAT fields except for GT and PL
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344 bcftools annotate -x INFO,^FORMAT/GT,FORMAT/PL file.vcf
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345
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346 # Add ID, QUAL and INFO/TAG, not replacing TAG if already present
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347 bcftools annotate -a src.bcf -c ID,QUAL,+TAG dst.bcf
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348
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349 # Carry over all INFO and FORMAT annotations except FORMAT/GT
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350 bcftools annotate -a src.bcf -c INFO,^FORMAT/GT dst.bcf
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351
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352 # Annotate from a tab-delimited file with six columns (the fifth is ignored),
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353 # first indexing with tabix. The coordinates are 1-based.
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354 tabix -s1 -b2 -e2 annots.tab.gz
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355 bcftools annotate -a annots.tab.gz -h annots.hdr -c CHROM,POS,REF,ALT,-,TAG file.vcf
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356
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357 # Annotate from a tab-delimited file with regions (1-based coordinates, inclusive)
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358 tabix -s1 -b2 -e3 annots.tab.gz
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359 bcftools annotate -a annots.tab.gz -h annots.hdr -c CHROM,FROM,TO,TAG inut.vcf
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360
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361 # Annotate from a bed file (0-based coordinates, half-closed, half-open intervals)
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362 bcftools annotate -a annots.bed.gz -h annots.hdr -c CHROM,FROM,TO,TAG input.vcf
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363
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364 @REGIONS_HELP@
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365 @EXPRESSIONS_HELP@
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366
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367 @BCFTOOLS_MANPAGE@#@EXECUTABLE@
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368
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369 @BCFTOOLS_WIKI@
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370 ]]>
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371 </help>
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372 <expand macro="citations" />
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373 </tool>