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comparison bcftools_csq.xml @ 0:2a6c13f8cc5a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
author iuc
date Thu, 13 Apr 2017 17:47:16 -0400
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1 <?xml version='1.0' encoding='utf-8'?>
2 <tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@VERSION@.0">
3 <description>Haplotype aware consequence predictor</description>
4 <macros>
5 <token name="@EXECUTABLE@">csq</token>
6 <import>macros.xml</import>
7 </macros>
8 <expand macro="requirements">
9 <expand macro="samtools_requirement"/>
10 </expand>
11 <expand macro="version_command" />
12 <command detect_errors="aggressive"><![CDATA[
13 @PREPARE_ENV@
14 @PREPARE_INPUT_FILE@
15 #set $section = $sec_required
16 @PREPARE_FASTA_REF@
17
18 #set $section = $sec_restrict
19 @PREPARE_TARGETS_FILE@
20 @PREPARE_REGIONS_FILE@
21
22 bcftools @EXECUTABLE@
23
24 ## csq required inputs section
25 #set $section = $sec_required
26 @FASTA_REF@
27 --gff-annot '$section.gff_annot'
28
29 ## csq options section
30 #set $section = $sec_csq_opts
31 #if str($section.ncsq):
32 --ncsq $section.ncsq
33 #end if
34 $section.local_csq
35 #if $section.phase:
36 --phase $section.phase
37 #end if
38 #if str($section.custom_tag):
39 --custom-tag '$section.custom_tag'
40 #end if
41
42 ## Subset section
43 #set $section = $sec_subset
44 @SAMPLES@
45
46 ## Filter section
47 #set $section = $sec_restrict
48 @INCLUDE@
49 @EXCLUDE@
50 @REGIONS@
51 @TARGETS@
52
53 @OUTPUT_TYPE@
54
55 ## Primary Input/Outputs
56 @INPUT_FILE@
57 > '$output_file'
58
59 ]]>
60 </command>
61 <inputs>
62 <expand macro="macro_input" />
63 <section name="sec_required" expanded="true" title="Required References">
64 <expand macro="macro_fasta_ref" />
65 <param name="gff_annot" type="data" format="gff3" label="GFF3 annotation file"
66 help="From Ensembl: ftp://ftp.ensembl.org/pub/current_gff3/"/>
67 </section>
68 <section name="sec_csq_opts" expanded="true" title="CSQ Options">
69 <param name="ncsq" type="integer" value="16" min="1" max="50" label="maximum number of consequences to consider per site"
70 help="-ncsq 16"/>
71 <param name="local_csq" type="boolean" truevalue="--local-csq" falsevalue="" checked="false" label="run localized predictions considering only one VCF record at a time"
72 help="--local-csq switch off haplotype-aware calling, run localized predictions considering only one VCF record at a time"/>
73 <param name="phase" type="select" optional="true" label="phase"
74 help="how to construct haplotypes and how to deal with unphased data">
75 <option value="a">take GTs as is, create haplotypes regardless of phase (0/1 -> 0|1)</option>
76 <option value="m">merge *all* GTs into a single haplotype (0/1 -> 1, 1/2 -> 1)</option>
77 <option value="r">require phased GTs, throw an error on unphased het GTs</option>
78 <option value="R">create non-reference haplotypes if possible (0/1 -> 1|1, 1/2 -> 1|2)</option>
79 <option value="s">skip unphased GTs</option>
80 </param>
81 <param name="custom_tag" type="text" value="" optional="true"
82 label="use this custom tag to store consequences rather than the default BCSQ tag">
83 <validator type="regex" message="">^(\w+)?$</validator>
84 </param>
85 </section>
86
87 <section name="sec_restrict" expanded="false" title="Restrict to">
88 <expand macro="macro_regions" />
89 <expand macro="macro_targets" />
90 <expand macro="macro_include" />
91 <expand macro="macro_exclude" />
92 </section>
93 <section name="sec_subset" expanded="false" title="Subset Options">
94 <expand macro="macro_samples" />
95 </section>
96 <expand macro="macro_select_output_type" />
97 </inputs>
98 <outputs>
99 <expand macro="macro_vcf_output" />
100 </outputs>
101 <tests>
102 <test>
103 <param name="input_file" ftype="vcf" value="csq.vcf" />
104 <param name="fasta_ref" ftype="fasta" value="csq.fa" />
105 <param name="gff_annot" ftype="gff3" value="csq.gff3" />
106 <param name="output_type" value="v" />
107 <output name="output_file">
108 <assert_contents>
109 <has_text text="BCSQ" />
110 </assert_contents>
111 </output>
112 </test>
113 </tests>
114 <help><![CDATA[
115 =====================================
116 bcftools @EXECUTABLE@
117 =====================================
118
119 Haplotype aware consequence predictor which correctly handles combined variants such as MNPs split over
120 multiple VCF records, SNPs separated by an intron (but adjacent in the spliced transcript) or nearby
121 frame-shifting indels which in combination in fact are not frame-shifting.
122
123 The output VCF is annotated with INFO/BCSQ and FORMAT/BCSQ tag (configurable with the -c option).
124 The latter is a bitmask of indexes to INFO/BCSQ, with interleaved haplotypes. See the usage examples
125 below for using the %TBCSQ converter in query for extracting a more human readable form from this bitmask.
126 The contruction of the bitmask limits the number of consequences that can be referenced in the FORMAT/BCSQ tags.
127 By default this is 16, but if more are required, see the --ncsq option.
128
129 The program requires on input a VCF/BCF file, the reference genome in fasta format (--fasta-ref)
130 and genomic features in the GFF3 format downloadable from the Ensembl website (--gff-annot),
131 and outputs an annotated VCF/BCF file. Currently, only Ensembl GFF3 files are supported.
132
133 By default, the input VCF should be phased. If phase is unknown, or only partially known,
134 the --phase option can be used to indicate how to handle unphased data. Alternatively,
135 haplotype aware calling can be turned off with the --local-csq option.
136
137 If conflicting (overlapping) variants within one haplotype are detected, a warning will
138 be emitted and predictions will be based on only the first variant in the analysis.
139
140 Symbolic alleles are not supported. They will remain unannotated in the output VCF and are
141 ignored for the prediction analysis.
142
143
144 @REGIONS_HELP@
145 @TARGETS_HELP@
146
147 @BCFTOOLS_MANPAGE@#@EXECUTABLE@
148
149 @BCFTOOLS_WIKI@
150 ]]>
151 </help>
152 <expand macro="citations" />
153 </tool>