Mercurial > repos > jjohnson > bcftools_annotate

annotate bcftools_annotate.xml @ 2:2943e6fe2221 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
author jjohnson
date Sun, 26 Jun 2016 15:46:12 -0400
parents 6c6a06ac35c1
children
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a30804010531 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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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="@VERSION@.0">
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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="requirements" />
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9 <expand macro="version_command" />
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10 <command detect_errors="aggressive"><![CDATA[
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11 @PREPARE_ENV@
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12 @PREPARE_INPUT_FILE@
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13 #set $annotation_file = None
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14 #set $annotation_hdr = None
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15 #set $section = $sec_annofile
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16 #if $section.annofile.anno_fmt == 'vcf':
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17 #set $annotation_file = 'annotations.vcf.gz'
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18 bgzip -c "$section.annofile.annotations" > $annotation_file &&
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19 bcftools index $annotation_file &&
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20 #elif $section.annofile.anno_fmt == 'tab':
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21 #if $section.annofile.annotations.ext == 'bed'
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22 #set $annotation_file = 'annotations.bed.gz'
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23 bgzip -c "$section.annofile.annotations" > $annotation_file &&
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24 tabix -s 1 -b 2 -e 3 $annotation_file &&
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25 #else:
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26 #set $annotation_file = 'annotations.tab.gz'
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27 bgzip -c "$section.annofile.annotations" > $annotation_file &&
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28 tabix -s 1 -b 2 -e 2 $annotation_file &&
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29 #end if
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30 #if $section.annofile.header_file:
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31 #set $annotation_hdr = $section.annofile.header_file
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32 #elif $section.annofile.header_lines:
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33 #set $annotation_hdr = 'annotation.hdr'
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34 grep '^\#\#INFO' ${hdr_file} > $annotation_hdr &&
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35 #end if
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36 #end if
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37
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38 bcftools @EXECUTABLE@
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39
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40 #set $section = $sec_annofile
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41 @COLUMNS@
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42 #if $annotation_file:
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43 --annotations "${annotation_file}"
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44 #end if
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45 #if $annotation_hdr:
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46 --header-lines "${annotation_hdr}"
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47 #end if
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48
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49 #if $section.set_id:
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50 --set-id "${section.set_id}"
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51 #end if
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52 #if $section.mark_sites:
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53 --mark-sites "${section.mark_sites}"
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54 #end if
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55
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56 #set $section = $sec_annotate
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57 #if $section.rename_chrs:
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58 --rename-chrs "${section.rename_chrs}"
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59 #end if
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60 #if $section.remove:
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61 --remove "${section.remove}"
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62 #end if
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63
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64 ## Default section
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65 #set $section = $sec_restrict
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66 @INCLUDE@
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67 @EXCLUDE@
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68 @REGIONS@
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69 @SAMPLES@
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70
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71 @OUTPUT_TYPE@
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72 @THREADS@
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73
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74 ## Primary Input/Outputs
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75 @INPUT_FILE@
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76 > "$output_file"
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77 ]]>
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78 </command>
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79 <configfiles>
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80 <configfile name="hdr_file"><![CDATA[#slurp
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81 #if $sec_annofile.annofile.anno_fmt == 'tab' and str($sec_annofile.annofile.header_lines) != '':
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82 $sec_annofile.annofile.header_lines.__str__.strip()#slurp
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83 #end if]]></configfile>
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84 </configfiles>
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85 <inputs>
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86 <expand macro="macro_input" />
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87 <section name="sec_annofile" expanded="false" title="Add Annotations">
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88 <expand macro="macro_columns" />
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89 <conditional name="annofile">
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90 <param name="anno_fmt" type="select" label="Annotations File">
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91 <option value="none">None</option>
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92 <option value="vcf">From a VCF/BCF file</option>
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93 <option value="tab">From a BED or tab-delimited file</option>
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94 </param>
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95 <when value="none"/>
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96 <when value="vcf">
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97 <param name="annotations" type="data" format="vcf" label="Annotations VCF"/>
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98 </when>
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99 <when value="tab">
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100 <param name="annotations" type="data" format="tabular,bed" label="Annotations">
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101 <help><![CDATA[
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102 BED, or a tab-delimited file with mandatory columns CHROM, POS (or, alternatively, FROM and TO),
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103 optional columns REF and ALT, and arbitrary number of annotation columns.
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104 Note that in case of tab-delimited file, the coordinates POS, FROM and TO are one-based and inclusive.
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105 ]]></help>
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106 </param>
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107 <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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108 <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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109 <help><![CDATA[
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110 ##INFO=<ID=NUMERIC_TAG,Number=1,Type=Integer,Description="Example header line">
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111 ##INFO=<ID=STRING_TAG,Number=1,Type=String,Description="Yet another header line">
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112 ]]></help>
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113 <sanitizer sanitize="False"/>
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114 </param>
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115 </when>
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116 </conditional>
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117 <param name="mark_sites" type="text" value="" label="Mark Sites TAG"
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118 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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119 <param name="set_id" type="text" value="" optional="true" label="Set Id">
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120 <help>Assign ID on the fly using the given format.
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121 By default all existing IDs are replaced.
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122 If the format string is preceded by "+", only missing IDs will be set.
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123 For example: '%CHROM\_%POS\_%REF\_%FIRST_ALT'
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124 </help>
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125 <sanitizer sanitize="False"/>
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126 <validator type="regex" message="">^([+]?(%[A-Z]+)(\_%[A-Z]+)*)?$</validator>
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127 </param>
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128 </section>
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129 <section name="sec_annotate" expanded="false" title="Change Annotations">
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130 <param name="remove" type="text" value="" label="Remove annotations" optional="true">
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131 <help><![CDATA[
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132 List of annotations to remove.
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133 Use "FILTER" to remove all filters or "FILTER/SomeFilter" to remove a specific filter.
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134 Similarly, "INFO" can be used to remove all INFO tags and "FORMAT" to remove all FORMAT tags except GT.
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135 To remove all INFO tags except "FOO" and "BAR", use "^INFO/FOO,INFO/BAR" (and similarly for FORMAT and FILTER).
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136 "INFO" can be abbreviated to "INF" and "FORMAT" to "FMT".
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137 ]]></help>
1
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138 <validator type="regex" message="">^(\^?[A-Z]+(/\w+)?(,\^?[A-Z]+(/\w+)?)*)?$</validator>
0
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139 </param>
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140 <param name="rename_chrs" type="data" format="tabular" label="Rename CHROM" optional="True"
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141 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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142 </section>
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143 <section name="sec_restrict" expanded="false" title="Restrict to">
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144 <expand macro="macro_include" />
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145 <expand macro="macro_exclude" />
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146 <expand macro="macro_regions" />
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147 <expand macro="macro_samples" />
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148 </section>
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149 <expand macro="macro_select_output_type" />
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150 </inputs>
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151 <outputs>
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152 <expand macro="macro_vcf_output"/>
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153 </outputs>
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154 <tests>
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155 <test>
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156 <param name="input_file" ftype="vcf" value="annotate.vcf" />
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157 <param name="anno_fmt" value="tab" />
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158 <param name="annotations" value="annotate.tab" />
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159 <param name="header_file" value="annotate.hdr" />
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160 <param name="columns" value="CHROM,POS,REF,ALT,ID,QUAL,INFO/T_INT,INFO/T_FLOAT,INDEL" />
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161 <param name="output_type" value="v" />
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162 <output name="output_file">
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163 <assert_contents>
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164 <has_text text="snp_3000150" />
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165 </assert_contents>
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166 </output>
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167 </test>
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168 <test>
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169 <param name="input_file" ftype="vcf" value="annotate.vcf" />
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170 <param name="anno_fmt" value="tab" />
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171 <param name="annotations" value="annotate2.tab" />
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172 <param name="header_file" value="annotate.hdr" />
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173 <param name="columns" value="CHROM,FROM,TO,T_STR" />
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174 <param name="output_type" value="v" />
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175 <output name="output_file">
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176 <assert_contents>
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177 <has_text text="T_STR=region_3000150_3106154" />
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178 </assert_contents>
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179 </output>
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180 </test>
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181 <test>
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182 <param name="input_file" ftype="vcf" value="annotate.vcf" />
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183 <param name="anno_fmt" value="vcf" />
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184 <param name="annotations" value="annots.vcf" />
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185 <param name="columns" value="STR,ID,QUAL,FILTER" />
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186 <param name="output_type" value="v" />
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187 <output name="output_file">
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188 <assert_contents>
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189 <has_text text="idIndel" />
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190 <has_text text="STR=testSNP" />
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191 </assert_contents>
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192 </output>
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193 </test>
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194 <test>
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195 <param name="input_file" ftype="vcf" value="annotate2.vcf" />
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196 <param name="anno_fmt" value="vcf" />
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197 <param name="annotations" value="annots2.vcf" />
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198 <param name="columns" value="ID,QUAL,FILTER,INFO,FMT" />
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199 <param name="output_type" value="v" />
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200 <output name="output_file">
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201 <assert_contents>
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202 <has_text text="q99" />
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203 <has_text text="FLAG;IINT=88,99;IFLT=8.8,9.9;ISTR=888,999" />
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204 </assert_contents>
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205 </output>
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206 </test>
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207 <test>
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208 <param name="input_file" ftype="vcf" value="annotate2.vcf" />
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209 <param name="anno_fmt" value="vcf" />
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210 <param name="annotations" value="annots2.vcf" />
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211 <param name="columns" value="ID,QUAL,FILTER,INFO,FMT" />
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212 <param name="samples" value="A" />
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213 <param name="output_type" value="v" />
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214 <output name="output_file">
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215 <assert_contents>
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216 <has_text text="q11" />
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217 <has_text text="FLAG;IINT=88,99;IFLT=8.8,9.9;ISTR=888,999" />
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218 </assert_contents>
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219 </output>
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220 </test>
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221 <test>
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222 <param name="input_file" ftype="vcf" value="annotate3.vcf" />
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223 <param name="anno_fmt" value="none" />
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224 <param name="remove" value="ID,QUAL,^FILTER/fltA,FILTER/fltB,^INFO/AA,INFO/BB,^FMT/GT,FMT/PL" />
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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>
1
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228 <not_has_text text="fltY" />
0
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229 </assert_contents>
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230 </output>
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231 </test>
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232 <test>
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233 <param name="input_file" ftype="vcf" value="annotate3.vcf" />
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234 <param name="anno_fmt" value="none" />
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235 <param name="remove" value="FORMAT" />
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236 <param name="output_type" value="v" />
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237 <output name="output_file">
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238 <assert_contents>
1
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239 <not_has_text text="GT:X:PL:Y:AA" />
0
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240 </assert_contents>
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241 </output>
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242 </test>
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243
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244 </tests>
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245 <help><![CDATA[
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246 ==================================
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247 bcftools @EXECUTABLE@
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248 ==================================
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249
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250 Annotate and edit VCF/BCF files.
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251
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252 Examples:
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253
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254 # Remove three fields
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255 bcftools annotate -x ID,INFO/DP,FORMAT/DP file.vcf.gz
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256
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257 # Remove all INFO fields and all FORMAT fields except for GT and PL
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258 bcftools annotate -x INFO,^FORMAT/GT,FORMAT/PL file.vcf
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259
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260 # Add ID, QUAL and INFO/TAG, not replacing TAG if already present
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261 bcftools annotate -a src.bcf -c ID,QUAL,+TAG dst.bcf
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262
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263 # Carry over all INFO and FORMAT annotations except FORMAT/GT
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264 bcftools annotate -a src.bcf -c INFO,^FORMAT/GT dst.bcf
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265
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266 # Annotate from a tab-delimited file with six columns (the fifth is ignored),
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267 # first indexing with tabix. The coordinates are 1-based.
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268 tabix -s1 -b2 -e2 annots.tab.gz
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269 bcftools annotate -a annots.tab.gz -h annots.hdr -c CHROM,POS,REF,ALT,-,TAG file.vcf
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270
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271 # Annotate from a tab-delimited file with regions (1-based coordinates, inclusive)
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272 tabix -s1 -b2 -e3 annots.tab.gz
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273 bcftools annotate -a annots.tab.gz -h annots.hdr -c CHROM,FROM,TO,TAG inut.vcf
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274
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275 # Annotate from a bed file (0-based coordinates, half-closed, half-open intervals)
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276 bcftools annotate -a annots.bed.gz -h annots.hdr -c CHROM,FROM,TO,TAG input.vcf
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277
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278 @REGIONS_HELP@
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279 @EXPRESSIONS_HELP@
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280
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281 @BCFTOOLS_MANPAGE@#@EXECUTABLE@
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282
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283 @BCFTOOLS_WIKI@
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284 ]]>
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285 </help>
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286 <expand macro="citations" />
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287 </tool>