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comparison bcftools_plugin_split_vep.xml @ 0:3b764ade1c6a 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 13:15:38 +0000
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children 5105faf7e04c
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-1:000000000000 0:3b764ade1c6a
1 <?xml version='1.0' encoding='utf-8'?>
2 <tool name="bcftools @EXECUTABLE@" id="bcftools_plugin_@PLUGIN_ID@" version="@TOOL_VERSION@">
3 <description>plugin Extracts fields from structured annotations such as INFO/CSQ</description>
4 <macros>
5 <token name="@EXECUTABLE@">split-vep</token>
6 <token name="@PLUGIN_ID@">split_vep</token>
7 <import>macros.xml</import>
8 </macros>
9 <expand macro="bio_tools" />
10 <expand macro="requirements" />
11 <expand macro="version_command" />
12 <command detect_errors="aggressive"><![CDATA[
13 @PREPARE_ENV@
14 @PREPARE_INPUT_FILE@
15 #set $section = $sec_restrict
16 @PREPARE_TARGETS_FILE@
17 @PREPARE_REGIONS_FILE@
18
19 bcftools plugin @EXECUTABLE@
20 ## VCF input section
21 #set $section = $sec_restrict
22 @INCLUDE@
23 @EXCLUDE@
24 @REGIONS@
25 @TARGETS@
26
27 @OUTPUT_TYPE@
28
29 ## Primary Input/Outputs
30 @INPUT_FILE@
31 ## Plugin options
32 ## ToDo: Parameters not wrapped yet: -A, -f (not for BCF/VCF output!), -l, -S, -x
33 -a '$a'
34 -c '$c'
35 $d
36 #if $p:
37 -p '$p'
38 #end if
39 #if $s:
40 -s '$s'
41 #end if
42 > '$output_file'
43 ]]>
44 </command>
45 <inputs>
46 <expand macro="macro_input" />
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." />
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." />
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="" />
50 <param argument="-p" type="text" optional="true" label="Enter prefix of INFO annotations to be created after splitting the CSQ string (optional)" />
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." />
52
53 <section name="sec_restrict" expanded="false" title="Restrict to">
54 <expand macro="macro_restrict" />
55 <expand macro="macro_restrict" type="target" label_type="Target" />
56 <expand macro="macro_include" />
57 <expand macro="macro_exclude" />
58 </section>
59 <expand macro="macro_select_output_type" />
60 </inputs>
61 <outputs>
62 <expand macro="macro_vcf_output" />
63 </outputs>
64 <tests>
65 <test>
66 <param name="input_file" ftype="vcf" value="plugin2.vcf" />
67 <param name="a" value="ANN" />
68 <param name="c" value="IMPACT,gnomAD_AF:Float" />
69 <param name="p" value="NW_" />
70 <param name="s" value="worst" />
71 <param name="output_type" value="v" />
72 <output name="output_file" ftype="vcf">
73 <assert_contents>
74 <has_line_matching expression="##INFO=&lt;ID=NW_IMPACT,.+" />
75 <has_line_matching expression="##INFO=&lt;ID=NW_gnomAD_AF,.+" />
76 <has_line_matching expression=".+NW_IMPACT=MODERATE;NW_gnomAD_AF=0\.08.+" />
77 <has_line_matching expression=".+NW_IMPACT=LOW;NW_gnomAD_AF=0\.9443.+" />
78 <has_line_matching expression=".+NW_IMPACT=MODIFIER;NW_gnomAD_AF=\..+" />
79 </assert_contents>
80 </output>
81 </test>
82 </tests>
83 <help><![CDATA[
84 =====================================
85 bcftools @EXECUTABLE@ plugin
86 =====================================
87
88 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.
89
90 Examples::
91
92 # Extract Consequence, IMPACT and gene SYMBOL of the most severe consequence into
93 # INFO annotations starting with the prefix "vep". For brevity, the columns can
94 # be given also as 0-based indexes
95 bcftools +split-vep -c Consequence,IMPACT,SYMBOL -s worst -p vep file.vcf.gz
96 bcftools +split-vep -c 1-3 -s worst -p vep file.vcf.gz
97
98 # Extract gnomAD_AF subfield into a new INFO/gnomAD_AF annotation of Type=Float so that
99 # numeric filtering can be used.
100 bcftools +split-vep -c gnomAD_AF:Float file.vcf.gz -i 'gnomAD_AF<0.001'
101
102 # Similar to above, but add the annotation only if the consequence severity is missense
103 # or equivalent.
104 bcftools +split-vep -c gnomAD_AF:Float -s :missense file.vcf.gz
105
106 @REGIONS_HELP@
107 @TARGETS_HELP@
108 @EXPRESSIONS_HELP@
109
110 ]]></help>
111 <expand macro="citations" />
112 </tool>