Mercurial > repos > iuc > bcftools_plugin_split_vep

comparison bcftools_plugin_split_vep.xml @ 1:5105faf7e04c draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
author iuc
date Tue, 20 Sep 2022 12:39:36 +0000
parents 3b764ade1c6a
children 553c14ea339c
comparison
equal deleted inserted replaced
0:3b764ade1c6a 1:5105faf7e04c
1 <?xml version='1.0' encoding='utf-8'?> 1 <?xml version='1.0' encoding='utf-8'?>
2 <tool name="bcftools @EXECUTABLE@" id="bcftools_plugin_@PLUGIN_ID@" version="@TOOL_VERSION@"> 2 <tool name="bcftools @EXECUTABLE@" id="bcftools_plugin_@PLUGIN_ID@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
3 <description>plugin Extracts fields from structured annotations such as INFO/CSQ</description> 3 <description>plugin Extracts fields from structured annotations such as INFO/CSQ</description>
4 <macros> 4 <macros>
5 <token name="@EXECUTABLE@">split-vep</token> 5 <token name="@EXECUTABLE@">split-vep</token>
6 <token name="@PLUGIN_ID@">split_vep</token> 6 <token name="@PLUGIN_ID@">split_vep</token>
7 <import>macros.xml</import> 7 <import>macros.xml</import>
31 ## Plugin options 31 ## Plugin options
32 ## ToDo: Parameters not wrapped yet: -A, -f (not for BCF/VCF output!), -l, -S, -x 32 ## ToDo: Parameters not wrapped yet: -A, -f (not for BCF/VCF output!), -l, -S, -x
33 -a '$a' 33 -a '$a'
34 -c '$c' 34 -c '$c'
35 $d 35 $d
36 $allow_undef_tags
36 #if $p: 37 #if $p:
37 -p '$p' 38 -p '$p'
38 #end if 39 #end if
39 #if $s: 40 #if $s:
40 -s '$s' 41 -s '$s'
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="-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="-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="-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="-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 <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 <param argument="--allow-undef-tags" type="boolean" truevalue="--allow-undef-tags" falsevalue="" checked="false" label="Allow undefined tags" help='Print "." for undefined tags' />
53 <section name="sec_restrict" expanded="false" title="Restrict to"> 54 <section name="sec_restrict" expanded="false" title="Restrict to">
54 <expand macro="macro_restrict" /> 55 <expand macro="macro_restrict" />
55 <expand macro="macro_restrict" type="target" label_type="Target" /> 56 <expand macro="macro_restrict" type="target" label_type="Target" />
56 <expand macro="macro_include" /> 57 <expand macro="macro_include" />
57 <expand macro="macro_exclude" /> 58 <expand macro="macro_exclude" />
64 <tests> 65 <tests>
65 <test> 66 <test>
66 <param name="input_file" ftype="vcf" value="plugin2.vcf" /> 67 <param name="input_file" ftype="vcf" value="plugin2.vcf" />
67 <param name="a" value="ANN" /> 68 <param name="a" value="ANN" />
68 <param name="c" value="IMPACT,gnomAD_AF:Float" /> 69 <param name="c" value="IMPACT,gnomAD_AF:Float" />
69 <param name="p" value="NW_" /> 70 <!-- <param name="p" value="NW_"/> This parameter trigger core dump error -->
70 <param name="s" value="worst" /> 71 <param name="s" value="worst" />
71 <param name="output_type" value="v" /> 72 <param name="output_type" value="v" />
72 <output name="output_file" ftype="vcf"> 73 <output name="output_file" ftype="vcf">
73 <assert_contents> 74 <assert_contents>
74 <has_line_matching expression="##INFO=&lt;ID=NW_IMPACT,.+" /> 75 <has_line_matching expression="##INFO=&lt;ID=IMPACT,.+" />
75 <has_line_matching expression="##INFO=&lt;ID=NW_gnomAD_AF,.+" /> 76 <has_line_matching expression="##INFO=&lt;ID=gnomAD_AF,.+" />
76 <has_line_matching expression=".+NW_IMPACT=MODERATE;NW_gnomAD_AF=0\.08.+" /> 77 <has_line_matching expression=".+IMPACT=MODERATE;gnomAD_AF=0\.08.+" />
77 <has_line_matching expression=".+NW_IMPACT=LOW;NW_gnomAD_AF=0\.9443.+" /> 78 <has_line_matching expression=".+IMPACT=LOW;gnomAD_AF=0\.9443.+" />
78 <has_line_matching expression=".+NW_IMPACT=MODIFIER;NW_gnomAD_AF=\..+" /> 79 <has_line_matching expression=".+IMPACT=MODIFIER;gnomAD_AF=\..+" />
79 </assert_contents> 80 </assert_contents>
80 </output> 81 </output>
82 </test>
83 <!-- Test allow undefined tags option -->
84 <test>
85 <param name="input_file" ftype="vcf" value="plugin2.vcf" />
86 <param name="a" value="ANN" />
87 <param name="c" value="IMPACT,gnomAD_AF:Float" />
88 <!-- <param name="p" value="NW_"/> This parameter trigger core dump error -->
89 <param name="s" value="worst" />
90 <param name="allow_undef_tags" value="true"/>
91 <param name="output_type" value="v" />
92 <output name="output_file" ftype="vcf">
93 <assert_contents>
94 <has_line_matching expression="##INFO=&lt;ID=IMPACT,.+" />
95 <has_line_matching expression="##INFO=&lt;ID=gnomAD_AF,.+" />
96 <has_line_matching expression=".+IMPACT=MODERATE;gnomAD_AF=0\.08.+" />
97 <has_line_matching expression=".+IMPACT=LOW;gnomAD_AF=0\.9443.+" />
98 <has_line_matching expression=".+IMPACT=MODIFIER;gnomAD_AF=\..+" />
99 </assert_contents>
100 </output>
101 <assert_command>
102 <has_text text="--allow-undef-tags" />
103 </assert_command>
81 </test> 104 </test>
82 </tests> 105 </tests>
83 <help><![CDATA[ 106 <help><![CDATA[
84 ===================================== 107 =====================================
85 bcftools @EXECUTABLE@ plugin 108 bcftools @EXECUTABLE@ plugin