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comparison annotate_variants.xml @ 0:fe2ff108038d draft

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author wolma
date Sat, 13 Dec 2014 17:19:26 -0500
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1 <tool id="annotate_variants" name="Variant Annotation">
2 <description>Predict the effects of SNPs and indels on known genes in the reference genome using SnpEff</description>
3 <requirements>
4 <requirement type="package" version="0.1.5">mimodd</requirement>
5 </requirements>
6 <version_command>mimodd version -q</version_command>
7 <command>
8 mimodd annotate
9
10 $inputfile
11
12 #if $str($annotool.name)=='snpeff':
13 --genome "${annotool.genomeVersion}"
14 #if $annotool.ori_output:
15 --snpeff-out $snpeff_file
16 #end if
17 #if $annotool.stats:
18 --stats $summary_file
19 #end if
20 ${annotool.snpeff_settings.chr} ${annotool.snpeff_settings.no_us} ${annotool.snpeff_settings.no_ds} ${annotool.snpeff_settings.no_intron} ${annotool.snpeff_settings.no_intergenic} ${annotool.snpeff_settings.no_utr}
21 #if $annotool.snpeff_settings.min_cov:
22 --minC ${annotool.snpeff_settings.min_cov}
23 #end if
24 #if $annotool.snpeff_settings.min_qual:
25 --minQ ${annotool.snpeff_settings.min_qual}
26 #end if
27 #if $annotool.snpeff_settings.ud:
28 --ud ${annotool.snpeff_settings.ud}
29 #end if
30 #end if
31
32 --ofile $outputfile
33 #if $str($formatting.oformat) == "text":
34 --oformat text
35 #end if
36 #if $str($formatting.oformat) == "html":
37 #if $formatting.formatter_file:
38 --link ${formatting.formatter_file}
39 #end if
40 #if $formatting.species
41 --species "${formatting.species}"
42 #end if
43 #end if
44
45 #if $str($grouping):
46 --grouping $grouping
47 #end if
48 --verbose
49 </command>
50
51 <inputs>
52 <param name="inputfile" type="data" format="vcf" label="vcf inputfile to be annotated" />
53 <param name="grouping" type="select" label="Group variants by">
54 <option value="">order in the input file</option>
55 <option value="by_sample">sample</option>
56 <option value="by_genes">most affected genes</option>
57 </param>
58 <conditional name="formatting">
59 <param name="oformat" type="select" label="Format of the annotation output file">
60 <option value="html">HTML</option>
61 <option value="text">Tab-separated plain text</option>
62 </param>
63 <when value="html">
64 <param name="formatter_file" type="data" format="txt" optional="true" label="Optional file with hyperlink formatting instructions" />
65 <param name="species" type="text" label="Species" help="Overwrite the species guess from the SnpEff genome, often not necessary" />
66 </when>
67 </conditional>
68 <conditional name="annotool">
69 <param name="name" type="select" label="Use this tool to annotate the input file" help = "Select SnpEff here, if you want to have the vcf input annotated with genomic feature information. Select None if you do not want additional annotation, if you do not have SnpEff installed, or if you have no appropriate SnpEff annotation file for the input.">
70 <option value="snpeff">SnpEff</option>
71 <option value="None">None</option>
72 </param>
73 <when value="snpeff">
74 <param name="genome_list" type="data" format="tabular" label="genome list" />
75 <param name="genomeVersion" type="select" label="Genome">
76 <options from_dataset="genome_list">
77 <column name="name" index="0"/>
78 <column name="value" index="1"/>
79 </options>
80 </param>
81 <param name="ori_output" type="boolean" checked="true" label="Keep the original SnpEff output" />
82 <param name="stats" type="boolean" checked="true" label="Produce a summary file of results" />
83
84 <conditional name="snpeff_settings">
85 <param name="detail_level" type="select" label="SnpEff-specific parameter settings" help="This section lets you specify the detailed parameter settings for the SnpEff tool.">
86 <option value="default">default settings</option>
87 <option value="change">change settings</option>
88 </param>
89 <when value="default">
90 ## default settings for SnpEff
91 <param name="chr" type="hidden" value=""/>
92 <param name="min_cov" type="hidden" value=""/>
93 <param name="min_qual" type="hidden" value=""/>
94 <param name="no_ds" type="hidden" value=""/>
95 <param name="no_us" type="hidden" value=""/>
96 <param name="no_intron" type="hidden" value=""/>
97 <param name="no_intergenic" type="hidden" value=""/>
98 <param name="no_utr" type="hidden" value=""/>
99 <param name="ud" type="hidden" value=""/>
100 </when>
101 <when value="change">
102 <param name="chr" type="boolean" truevalue="-chr" falsevalue="" checked="false" label="prepend 'chr' to chromosome names, e.g., 'chr7' instead of '7'" />
103 <param name="min_cov" type="integer" optional="true" label="minimum coverage (default = not used)" help="do not include variants with a coverage lower than this value"/>
104 <param name="min_qual" type="integer" optional="true" label="minimum quality (default = not used)" help="do not include variants with a quality lower than this value"/>
105 <param name="no_ds" type="boolean" label="do not show downstream changes" truevalue="--no-downstream" falsevalue="" checked="false" help="annotation of effects on the downstream region of genes can be suppressed"/>
106 <param name="no_us" type="boolean" label="do not show upstream changes" truevalue="--no-upstream" falsevalue="" checked="false" help="annotation of effects on the upstream region of genes can be suppressed"/>
107 <param name="no_intron" type="boolean" label="do not show intron changes" truevalue="--no-intron" falsevalue="" checked="false" help="annotation of effects on introns of genes can be suppressed"/>
108 <param name="no_intergenic" type="boolean" label="do not show intergenic changes" truevalue="--no-intergenic" falsevalue="" checked="false" help="annotation of effects on intergenic regions can be suppressed"/>
109 <param name="no_utr" type="boolean" label="do not show UTR changes" truevalue="--no-utr" falsevalue="" checked="false" help="annotation of effects on the untranslated regions of genes can be suppressed"/>
110 <param name="ud" type="integer" optional="true" label="upstream downstream interval length (default = 5000 bases)" help="specify the upstream/downstream interval length, i.e., variants more than INTERVAL nts from the next annotated gene are considered to be intergenic"/>
111 </when>
112 </conditional>
113 </when>
114 </conditional>
115 </inputs>
116
117 <outputs>
118 <data name="outputfile" format="html" >
119 <change_format>
120 <when input="formatting.oformat" value="text" format="tabular"/>
121 </change_format>
122 </data>
123 <data name="snpeff_file" format="vcf" >
124 <filter>(annotool['name']=="snpeff" and annotool['ori_output'])</filter>
125 </data>
126 <data name="summary_file" format="html">
127 <filter>(annotool['name']=="snpeff" and annotool['stats'])</filter>
128 </data>
129 </outputs>
130
131 <help>
132 .. class:: infomark
133
134 **What it does**
135
136 The tool turns a variant list in VCF format into a more readable summary table listing variant sites and effects.
137
138 If installed, the variant annotation tool SnpEff can be used transparently to determine the genomic features, e.g., genes or transcripts, affected by the variants.
139
140 Use of this feature requires that you have an appropriate SnpEff genome file installed on the host machine. You can use the *List installed SnpEff genomes* tool to generate a list of all available SnpEff genomes.
141 This list can then be used (by selecting the dataset as the *genome list*) to populate the *genome* dropdown menu, from which you can select the SnpEff genome file to be used for the annotation.
142
143 As output file formats HTML or plain text are supported.
144 In HTML mode, variant positions and/or affected genomic features can be turned into hyperlinks to corresponding views in web-based genome browsers and databases.
145
146 The behavior of this feature depends on:
147
148 1) Recognition of the species that is analyzed
149
150 You can declare the species you are working with using the *Species* text field.
151 If you are not declaring the species explicitly, but are choosing SnpEff for effect annotation, the tool will usually be able to auto-detect the species from the SnpEff genome you are using.
152 If no species gets assigned in either way, no hyperlinks will be generated and the html output will look essentially like plain text.
153
154 2) Available hyperlink formatting rules for this species
155
156 When the species has been recognized, the tool checks if you have selected an *optional file with hyperlink formatting instructions*.
157 If you did and that file contains an entry matching the recognized species, that entry will be used as a template to construct the hyperlinks.
158 If no matching entry is found in the file, an error will be raised.
159
160 If you did not supply a hyperlink formatting instruction file, the tool will consult an internal lookup table to see if it finds default rules for the construction of the hyperlinks for the species.
161 If not, no hyperlinks will be generated and the html output will look essentially like plain text.
162
163 **TIP:**
164 MiModD's internal hyperlink formatting lookup tables are maintained and growing with every new version, but since weblinks are changing frequently as well, it is possible that you will encounter broken hyperlinks for your species of interest. In such a case, you can resort to two things: `tell us about the problem`_ to make sure it gets fixed in the next release and, in the meantime, use a custom file with hyperlink formatting instructions to overwrite the default entry for your species.
165
166 .. _tell us about the problem: mailto:mimodd@googlegroups.com
167 </help>
168 </tool>
169