Mercurial > repos > iuc > bcftools_plugin_split_vep

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 784611c9caf2680d41414ca2880b93a69d719701
author iuc
date Sun, 18 Aug 2024 10:04:02 +0000
parents 70276425d001
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1 <tool name="bcftools @EXECUTABLE@" id="bcftools_plugin_@PLUGIN_ID@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>plugin Extracts fields from structured annotations such as INFO/CSQ</description>
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3 <macros>
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4 <token name="@EXECUTABLE@">split-vep</token>
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5 <token name="@PLUGIN_ID@">split_vep</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 $section = $sec_restrict
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15 @PREPARE_TARGETS_FILE@
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16 @PREPARE_REGIONS_FILE@
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18 bcftools plugin @EXECUTABLE@
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19 ## VCF input section
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20 #set $section = $sec_restrict
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21 @INCLUDE@
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22 @EXCLUDE@
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23 @REGIONS@
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24 @TARGETS@
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26 @OUTPUT_TYPE@
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27
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28 ## Primary Input/Outputs
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29 @INPUT_FILE@
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30 ## Plugin options
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31 ## ToDo: Parameters not wrapped yet: -A, -f (not for BCF/VCF output!), -l, -S, -x
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32 -a '$a'
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33 -c '$c'
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34 $d
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35 $allow_undef_tags
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36 #if $p:
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37 -p '$p'
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38 #end if
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39 #if $s:
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40 -s '$s'
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41 #end if
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42 > '$output_file'
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43 ]]>
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44 </command>
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45 <inputs>
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46 <expand macro="macro_input" />
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47 <param argument="-a" type="text" value="CSQ" label="Select INFO annotation to parse" help="Usually, annotations are located in the CSQ, ANN or EFF INFO field, though any arbitrary tag may be entered here." />
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48 <param argument="-c" type="text" label="Enter fields to be extracted, listed either as indexes or names" help="The default type of the new annotation is String but can be also set to Integer/Int or Float/Real by adding ':type' to the field name or index. Examples can be found in the tool help." />
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49 <param argument="-d" type="boolean" label="Enable Output per transcript/allele consequences on a new line rather rather than as comma-separated fields on a single line" truevalue="-d" falsevalue="" />
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50 <param argument="-p" type="text" optional="true" label="Enter prefix of INFO annotations to be created after splitting the CSQ string (optional)" />
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51 <param argument="-s" type="text" optional="true" label="Select transcripts to extract by type and/or consequence (optional)" help="Argument has the form TR:CSQ. TR = transcript: worst,primary,all (default: all). CSQ = consequence: any,missense,missense+,etc (default: any). Examples can be found in the tool help." />
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52 <param argument="--allow-undef-tags" type="boolean" truevalue="--allow-undef-tags" falsevalue="" checked="false" label="Allow undefined tags" help='Print "." for undefined tags' />
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53 <section name="sec_restrict" expanded="false" title="Restrict to">
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54 <expand macro="macro_restrict" />
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55 <expand macro="macro_restrict" type="target" label_type="Target" />
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56 <expand macro="macro_include" />
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57 <expand macro="macro_exclude" />
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58 </section>
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59 <expand macro="macro_select_output_type" />
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60 </inputs>
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61 <outputs>
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62 <expand macro="macro_vcf_output" />
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63 </outputs>
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64 <tests>
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65 <test>
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66 <param name="input_file" ftype="vcf" value="plugin2.vcf" />
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67 <param name="a" value="ANN" />
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68 <param name="c" value="IMPACT,gnomAD_AF:Float" />
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69 <!-- <param name="p" value="NW_"/> This parameter trigger core dump error -->
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70 <param name="s" value="worst" />
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71 <param name="output_type" value="v" />
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72 <output name="output_file" ftype="vcf">
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73 <assert_contents>
1
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74 <has_line_matching expression="##INFO=&lt;ID=IMPACT,.+" />
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75 <has_line_matching expression="##INFO=&lt;ID=gnomAD_AF,.+" />
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76 <has_line_matching expression=".+IMPACT=MODERATE;gnomAD_AF=0\.08.+" />
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77 <has_line_matching expression=".+IMPACT=LOW;gnomAD_AF=0\.9443.+" />
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78 <has_line_matching expression=".+IMPACT=MODIFIER;gnomAD_AF=\..+" />
0
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79 </assert_contents>
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80 </output>
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81 </test>
1
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82 <!-- Test allow undefined tags option -->
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83 <test>
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84 <param name="input_file" ftype="vcf" value="plugin2.vcf" />
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85 <param name="a" value="ANN" />
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86 <param name="c" value="IMPACT,gnomAD_AF:Float" />
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87 <!-- <param name="p" value="NW_"/> This parameter trigger core dump error -->
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88 <param name="s" value="worst" />
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89 <param name="allow_undef_tags" value="true"/>
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90 <param name="output_type" value="v" />
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91 <output name="output_file" ftype="vcf">
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92 <assert_contents>
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93 <has_line_matching expression="##INFO=&lt;ID=IMPACT,.+" />
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94 <has_line_matching expression="##INFO=&lt;ID=gnomAD_AF,.+" />
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95 <has_line_matching expression=".+IMPACT=MODERATE;gnomAD_AF=0\.08.+" />
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96 <has_line_matching expression=".+IMPACT=LOW;gnomAD_AF=0\.9443.+" />
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97 <has_line_matching expression=".+IMPACT=MODIFIER;gnomAD_AF=\..+" />
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98 </assert_contents>
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99 </output>
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100 <assert_command>
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101 <has_text text="--allow-undef-tags" />
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102 </assert_command>
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103 </test>
0
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104 </tests>
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105 <help><![CDATA[
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106 =====================================
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107 bcftools @EXECUTABLE@ plugin
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108 =====================================
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109
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110 This plugin allows to extract fields from structured annotations such as ``INFO/CSQ`` created by bcftools/csq or VEP. These fields are then added to the VCF as new ``INFO`` fields.
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111
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112 Examples::
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113
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114 # Extract Consequence, IMPACT and gene SYMBOL of the most severe consequence into
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115 # INFO annotations starting with the prefix "vep". For brevity, the columns can
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116 # be given also as 0-based indexes
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117 bcftools +split-vep -c Consequence,IMPACT,SYMBOL -s worst -p vep file.vcf.gz
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118 bcftools +split-vep -c 1-3 -s worst -p vep file.vcf.gz
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119
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120 # Extract gnomAD_AF subfield into a new INFO/gnomAD_AF annotation of Type=Float so that
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121 # numeric filtering can be used.
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122 bcftools +split-vep -c gnomAD_AF:Float file.vcf.gz -i 'gnomAD_AF<0.001'
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123
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124 # Similar to above, but add the annotation only if the consequence severity is missense
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125 # or equivalent.
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126 bcftools +split-vep -c gnomAD_AF:Float -s :missense file.vcf.gz
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127
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128 @REGIONS_HELP@
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129 @TARGETS_HELP@
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130 @EXPRESSIONS_HELP@
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131
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132 ]]></help>
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133 <expand macro="citations" />
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134 </tool>