Mercurial > repos > iuc > bcftools_annotate

annotate bcftools_annotate.xml @ 16:e075b1be5abb draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit c45135e52ae5039e09272ac6f504d0ceb574aa70
author iuc
date Sat, 23 Jul 2022 13:36:16 +0000
parents 2958e3b49ad4
children 8a2e296c07ef
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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@+galaxy1">
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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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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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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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69 #set $section = $sec_annotate
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70 #if $section.rename_chrs:
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71 --rename-chrs '${section.rename_chrs}'
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72 #end if
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73 #if $section.remove:
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74 --remove '${section.remove}'
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75 #end if
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77 ## Default section
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78 #set $section = $sec_restrict
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79 @INCLUDE@
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80 @EXCLUDE@
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81 @COLLAPSE@
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82 @REGIONS@
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83 @SAMPLES@
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84
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85 @OUTPUT_TYPE@
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86 @THREADS@
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87
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88 ## Primary Input/Outputs
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89 @INPUT_FILE@
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90 > '$output_file'
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91 ]]>
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92 </command>
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93 <configfiles>
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94 <configfile name="hdr_file"><![CDATA[#slurp
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95 #if $sec_annofile.annofile.anno_fmt == 'tab' and str($sec_annofile.annofile.header_lines) != '':
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96 $sec_annofile.annofile.header_lines.__str__.strip()#slurp
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97 #end if]]></configfile>
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98 </configfiles>
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99 <inputs>
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100 <expand macro="macro_input" />
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101 <section name="sec_annofile" expanded="false" title="Add Annotations">
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102 <expand macro="macro_columns" />
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103 <conditional name="annofile">
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104 <param name="anno_fmt" type="select" label="Annotations File">
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105 <option value="none">None</option>
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106 <option value="vcf">From a VCF/BCF file</option>
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107 <option value="tab">From a BED or tab-delimited file</option>
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108 </param>
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109 <when value="none"/>
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110 <when value="vcf">
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111 <param name="annotations" type="data" format="vcf,bcf" label="Annotations VCF"/>
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112 </when>
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113 <when value="tab">
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114 <param name="annotations" type="data" format="tabular,bed" label="Annotations">
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115 <help><![CDATA[
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116 BED, or a tab-delimited file with mandatory columns CHROM, POS (or, alternatively, FROM and TO),
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117 optional columns REF and ALT, and arbitrary number of annotation columns.
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118 Note that in case of tab-delimited file, the coordinates POS, FROM and TO are one-based and inclusive.
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119 ]]></help>
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120 </param>
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121 <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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122 <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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123 <help><![CDATA[
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124 ##INFO=<ID=NUMERIC_TAG,Number=1,Type=Integer,Description="Example header line">
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125 ##INFO=<ID=STRING_TAG,Number=1,Type=String,Description="Yet another header line">
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126 ]]></help>
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127 <sanitizer sanitize="False"/>
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128 </param>
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129 </when>
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130 </conditional>
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131 <param argument="--mark-sites" type="text" value="" label="Mark Sites TAG"
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132 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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133 <param argument="--set-id" type="text" value="" optional="true" label="Set Id">
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134 <help>Assign ID on the fly using the given format.
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135 By default all existing IDs are replaced.
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136 If the format string is preceded by "+", only missing IDs will be set.
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137 For example: '%CHROM\_%POS\_%REF\_%FIRST_ALT'
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138 </help>
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139 <sanitizer sanitize="False"/>
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140 <validator type="regex" message="">^([+]?(%[A-Z_]+)(\\_%[A-Z_]+)*)?$</validator>
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141 </param>
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142 </section>
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143 <section name="sec_annotate" expanded="false" title="Change Annotations">
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144 <param argument="--remove" type="text" value="" label="Remove annotations" optional="true">
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145 <help><![CDATA[
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146 List of annotations to remove.
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147 Use "FILTER" to remove all filters or "FILTER/SomeFilter" to remove a specific filter.
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148 Similarly, "INFO" can be used to remove all INFO tags and "FORMAT" to remove all FORMAT tags except GT.
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149 To remove all INFO tags except "FOO" and "BAR", use "^INFO/FOO,INFO/BAR" (and similarly for FORMAT and FILTER).
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150 "INFO" can be abbreviated to "INF" and "FORMAT" to "FMT".
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151 ]]></help>
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152 <validator type="regex" message="">^(\^?[A-Z]+(/\w+)?(,\^?[A-Z]+(/\w+)?)*)?$</validator>
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153 </param>
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154 <param argument="--rename-chrs" type="data" format="tabular" label="Rename CHROM" optional="true"
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155 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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156 </section>
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157 <section name="sec_restrict" expanded="false" title="Restrict to">
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158 <expand macro="macro_include" />
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159 <expand macro="macro_exclude" />
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160 <expand macro="macro_collapse" />
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161 <expand macro="macro_restrict" />
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162 <expand macro="macro_samples" />
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163 </section>
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164 <expand macro="macro_select_output_type" />
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165 </inputs>
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166 <outputs>
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167 <expand macro="macro_vcf_output"/>
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168 </outputs>
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169 <tests>
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170 <test>
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171 <param name="input_file" ftype="vcf" value="annotate.vcf" />
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172 <param name="anno_fmt" value="tab" />
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173 <param name="annotations" value="annotate.tab" />
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174 <param name="header_file" value="annotate.hdr" />
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175 <param name="columns" value="CHROM,POS,REF,ALT,ID,QUAL,INFO/T_INT,INFO/T_FLOAT,INDEL" />
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176 <param name="output_type" value="v" />
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177 <output name="output_file">
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178 <assert_contents>
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179 <has_text text="snp_3000150" />
e58e34d48868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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180 </assert_contents>
e58e34d48868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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181 </output>
e58e34d48868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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182 </test>
e58e34d48868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
183 <test>
e58e34d48868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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diff changeset
184 <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
185 <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
186 <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
187 <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
188 <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
189 <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
190 <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
191 </conditional>
2958e3b49ad4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ccc967cdce26379110361f8dea521bade23f8612"
iuc
parents: 14
diff changeset
192 <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
193 </section>
0
e58e34d48868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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diff changeset
194 <param name="output_type" value="v" />
e58e34d48868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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195 <output name="output_file">
e58e34d48868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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196 <assert_contents>
e58e34d48868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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197 <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
198 <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
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199 </assert_contents>
e58e34d48868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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diff changeset
200 </output>
e58e34d48868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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diff changeset
201 </test>
e58e34d48868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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diff changeset
202 <test>
e58e34d48868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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diff changeset
203 <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
204 <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
205 <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
206 <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
207 <param name="output_type" value="v" />
e58e34d48868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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diff changeset
208 <output name="output_file">
e58e34d48868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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diff changeset
209 <assert_contents>
e58e34d48868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
210 <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
211 <has_text text="STR=testSNP" />
e58e34d48868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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diff changeset
212 </assert_contents>
e58e34d48868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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diff changeset
213 </output>
e58e34d48868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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214 </test>
e58e34d48868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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215 <test>
9
a80ec64f9101 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 942ca2971ae6a72e548fde6186c6408a1e236653
iuc
parents: 8
diff changeset
216 <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
217 <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
218 <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
219 <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
220 <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
221 <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
222 <assert_contents>
a80ec64f9101 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 942ca2971ae6a72e548fde6186c6408a1e236653
iuc
parents: 8
diff changeset
223 <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
224 <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
225 </assert_contents>
a80ec64f9101 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 942ca2971ae6a72e548fde6186c6408a1e236653
iuc
parents: 8
diff changeset
226 </output>
a80ec64f9101 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 942ca2971ae6a72e548fde6186c6408a1e236653
iuc
parents: 8
diff changeset
227 </test>
a80ec64f9101 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 942ca2971ae6a72e548fde6186c6408a1e236653
iuc
parents: 8
diff changeset
228 <test>
0
e58e34d48868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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diff changeset
229 <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
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diff changeset
230 <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
231 <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
232 <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
233 <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
234 <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
235 <assert_contents>
e58e34d48868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
236 <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
237 <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
238 </assert_contents>
e58e34d48868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
239 </output>
e58e34d48868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
240 </test>
e58e34d48868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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diff changeset
241 <test>
e58e34d48868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
242 <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
243 <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
244 <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
245 <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
246 <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
247 <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
248 <output name="output_file">
e58e34d48868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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diff changeset
249 <assert_contents>
e58e34d48868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
250 <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
251 <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
252 </assert_contents>
e58e34d48868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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diff changeset
253 </output>
e58e34d48868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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diff changeset
254 </test>
e58e34d48868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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diff changeset
255 <test>
e58e34d48868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
256 <param name="input_file" ftype="vcf" value="annotate3.vcf" />
e58e34d48868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
257 <param name="anno_fmt" value="none" />
e58e34d48868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
258 <param name="remove" value="ID,QUAL,^FILTER/fltA,FILTER/fltB,^INFO/AA,INFO/BB,^FMT/GT,FMT/PL" />
e58e34d48868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
259 <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
260 <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
261 <assert_contents>
e58e34d48868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
262 <not_has_text text="fltY" />
e58e34d48868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
263 </assert_contents>
e58e34d48868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
264 </output>
e58e34d48868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
265 </test>
e58e34d48868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
266 <test>
e58e34d48868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
267 <param name="input_file" ftype="vcf" value="annotate3.vcf" />
e58e34d48868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
268 <param name="anno_fmt" value="none" />
e58e34d48868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
269 <param name="remove" value="FORMAT" />
e58e34d48868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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diff changeset
270 <param name="output_type" value="v" />
e58e34d48868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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271 <output name="output_file">
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272 <assert_contents>
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273 <not_has_text text="GT:X:PL:Y:AA" />
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274 </assert_contents>
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275 </output>
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276 </test>
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277
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278 </tests>
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279 <help><![CDATA[
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280 ==================================
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281 bcftools @EXECUTABLE@
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282 ==================================
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283
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284 Annotate and edit VCF/BCF files.
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285
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286 Examples:
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287
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288 # Remove three fields
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289 bcftools annotate -x ID,INFO/DP,FORMAT/DP file.vcf.gz
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290
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291 # Remove all INFO fields and all FORMAT fields except for GT and PL
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292 bcftools annotate -x INFO,^FORMAT/GT,FORMAT/PL file.vcf
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293
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294 # Add ID, QUAL and INFO/TAG, not replacing TAG if already present
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295 bcftools annotate -a src.bcf -c ID,QUAL,+TAG dst.bcf
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296
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297 # Carry over all INFO and FORMAT annotations except FORMAT/GT
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298 bcftools annotate -a src.bcf -c INFO,^FORMAT/GT dst.bcf
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299
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300 # Annotate from a tab-delimited file with six columns (the fifth is ignored),
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301 # first indexing with tabix. The coordinates are 1-based.
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302 tabix -s1 -b2 -e2 annots.tab.gz
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303 bcftools annotate -a annots.tab.gz -h annots.hdr -c CHROM,POS,REF,ALT,-,TAG file.vcf
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304
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305 # Annotate from a tab-delimited file with regions (1-based coordinates, inclusive)
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306 tabix -s1 -b2 -e3 annots.tab.gz
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307 bcftools annotate -a annots.tab.gz -h annots.hdr -c CHROM,FROM,TO,TAG inut.vcf
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308
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309 # Annotate from a bed file (0-based coordinates, half-closed, half-open intervals)
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310 bcftools annotate -a annots.bed.gz -h annots.hdr -c CHROM,FROM,TO,TAG input.vcf
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311
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312 @REGIONS_HELP@
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313 @EXPRESSIONS_HELP@
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314
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315 @BCFTOOLS_MANPAGE@#@EXECUTABLE@
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316
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317 @BCFTOOLS_WIKI@
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318 ]]>
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319 </help>
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320 <expand macro="citations" />
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321 </tool>