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comparison bcftools_plugin_frameshifts.xml @ 9:b14468416547 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
author iuc
date Wed, 05 Jun 2019 12:43:19 -0400
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children 758ce6301579
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8:9e945cdeb823 9:b14468416547
1 <?xml version='1.0' encoding='utf-8'?>
2 <tool name="bcftools @EXECUTABLE@" id="bcftools_plugin_@PLUGIN_ID@" version="@TOOL_VERSION@+galaxy1">
3 <description>plugin Annotate frameshift indels</description>
4 <macros>
5 <token name="@EXECUTABLE@">frameshifts</token>
6 <token name="@PLUGIN_ID@">frameshifts</token>
7 <import>macros.xml</import>
8 </macros>
9 <expand macro="requirements" />
10 <expand macro="version_command" />
11 <command detect_errors="aggressive"><![CDATA[
12 @PREPARE_ENV@
13 @PREPARE_INPUT_FILE@
14 #set $section = $sec_restrict
15 @PREPARE_TARGETS_FILE@
16 @PREPARE_REGIONS_FILE@
17 ## exons file needs to be bgzip and have tabix index
18 bgzip -c $exons > exons.bed.gz &&
19 tabix exons.bed.gz &&
20
21 bcftools plugin @EXECUTABLE@
22 ## VCF input section
23 #set $section = $sec_restrict
24 @INCLUDE@
25 @EXCLUDE@
26 @REGIONS@
27 @TARGETS@
28
29 @OUTPUT_TYPE@
30 @THREADS@
31
32 ## Primary Input/Outputs
33 @INPUT_FILE@
34 ## Plugin options
35 -- --exons exons.bed.gz
36 > '$output_file'
37 ]]>
38 </command>
39 <inputs>
40 <expand macro="macro_input" />
41 <param name="exons" type="data" format="bed"
42 label="Exons File" help="BED file describing exons" />
43 <section name="sec_restrict" expanded="false" title="Restrict to">
44 <expand macro="macro_restrict" />
45 <expand macro="macro_restrict" type="target" label_type="Target" />
46 <expand macro="macro_include" />
47 <expand macro="macro_exclude" />
48 </section>
49 <expand macro="macro_select_output_type" />
50 </inputs>
51 <outputs>
52 <expand macro="macro_vcf_output" />
53 </outputs>
54 <tests>
55 <test>
56 <param name="input_file" ftype="vcf" value="plugin1.vcf" />
57 <param name="exons" ftype="bed" value="plugin_frameshifts.bed" />
58 <param name="output_type" value="v" />
59 <output name="output_file" ftype="vcf">
60 <assert_contents>
61 <has_line_matching expression="##INFO=&lt;ID=OOF,.+" />
62 <has_line_matching expression="1&#09;3106154&#09;.&#09;CAAA&#09;C&#09;.+&#09;.+&#09;OOF=0.+" />
63 <has_line_matching expression="1&#09;3106154&#09;.&#09;C&#09;CT&#09;.+&#09;.+&#09;OOF=1.+" />
64 </assert_contents>
65 </output>
66 </test>
67 </tests>
68 <help><![CDATA[
69 =====================================
70 bcftools @EXECUTABLE@ plugin
71 =====================================
72
73 A simple tool to annotate the effect of indel variants.
74
75 Adds an ``OOF`` (out-of-frame) subfield to the ``INFO`` field of indel records
76 found in the input, where
77
78 - ``OOF=1`` indicates that the indel results in a frameshift
79 - ``OOF=0`` indicates an in-frame indel
80
81 The information about indel effects is extracted from the ``BED`` input, which
82 is supposed to describe the reference genome exons.
83
84 If a variant record lists several ``ALT`` alleles, some of them indels, then
85 ``OOF`` will be a comma-separated list of status indicators. In the list a
86 third ``OOF`` status code of ``-1`` will be used to indicate ``ALT`` alleles
87 that are not associated with a change in sequence length or that don't affect
88 an exon.
89
90 The formal definition (added to the VCF header) of the ``OOF`` subfield is::
91
92 INFO=<ID=OOF,Number=A,Type=Integer,Description="Frameshift Indels: out-of-frame (1), in-frame (0), not-applicable (-1 or missing)">
93
94 @REGIONS_HELP@
95 @TARGETS_HELP@
96 @EXPRESSIONS_HELP@
97
98 ]]></help>
99 <expand macro="citations" />
100 </tool>