annotate annotate_variants.xml @ 3:ba685c655e18

Uploaded
author wolma
date Wed, 11 Feb 2015 09:26:43 -0500
parents 72d20758ba2c
children bdd1995c9e66
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
1 <tool id="annotate_variants" name="Variant Annotation">
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
2 <description>Predict the effects of SNPs and indels on known genes in the reference genome using SnpEff</description>
2
72d20758ba2c final upload
wolma
parents: 1
diff changeset
3 <macros>
72d20758ba2c final upload
wolma
parents: 1
diff changeset
4 <import>toolshed_macros.xml</import>
72d20758ba2c final upload
wolma
parents: 1
diff changeset
5 </macros>
72d20758ba2c final upload
wolma
parents: 1
diff changeset
6 <expand macro="requirements"/>
0
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
7 <version_command>mimodd version -q</version_command>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
8 <command>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
9 mimodd annotate
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
10
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
11 "$inputfile"
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
12
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
13 #if $str($annotool.name)=='snpeff':
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
14 --genome "${annotool.genomeVersion}"
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
15 #if $annotool.ori_output:
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
16 --snpeff-out "$snpeff_file"
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
17 #end if
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
18 #if $annotool.stats:
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
19 --stats "$summary_file"
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
20 #end if
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
21 ${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}
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
22 #if $annotool.snpeff_settings.min_cov:
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
23 --minC "${annotool.snpeff_settings.min_cov}"
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
24 #end if
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
25 #if $annotool.snpeff_settings.min_qual:
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
26 --minQ "${annotool.snpeff_settings.min_qual}"
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
27 #end if
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
28 #if $annotool.snpeff_settings.ud:
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
29 --ud "${annotool.snpeff_settings.ud}"
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
30 #end if
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
31 #end if
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
32
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
33 --ofile "$outputfile"
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
34 #if $str($formatting.oformat) == "text":
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
35 --oformat text
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
36 #end if
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
37 #if $str($formatting.oformat) == "html":
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
38 #if $formatting.formatter_file:
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
39 --link "${formatting.formatter_file}"
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
40 #end if
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
41 #if $formatting.species
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
42 --species "${formatting.species}"
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
43 #end if
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
44 #end if
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
45
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
46 #if $str($grouping):
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
47 --grouping $grouping
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
48 #end if
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
49 --verbose
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
50 </command>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
51
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
52 <inputs>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
53 <param name="inputfile" type="data" format="vcf" label="vcf inputfile to be annotated" />
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
54 <param name="grouping" type="select" label="Group variants by">
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
55 <option value="">order in the input file</option>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
56 <option value="by_sample">sample</option>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
57 <option value="by_genes">most affected genes</option>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
58 </param>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
59 <conditional name="formatting">
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
60 <param name="oformat" type="select" label="Format of the annotation output file">
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
61 <option value="html">HTML</option>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
62 <option value="text">Tab-separated plain text</option>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
63 </param>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
64 <when value="html">
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
65 <param name="formatter_file" type="data" format="txt" optional="true" label="Optional file with hyperlink formatting instructions" />
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
66 <param name="species" type="text" label="Species" help="Overwrite the species guess from the SnpEff genome, often not necessary" />
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
67 </when>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
68 </conditional>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
69 <conditional name="annotool">
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
70 <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.">
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
71 <option value="snpeff">SnpEff</option>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
72 <option value="None">None</option>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
73 </param>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
74 <when value="snpeff">
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
75 <param name="genome_list" type="data" format="tabular" label="genome list" />
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
76 <param name="genomeVersion" type="select" label="Genome">
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
77 <options from_dataset="genome_list">
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
78 <column name="name" index="0"/>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
79 <column name="value" index="1"/>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
80 </options>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
81 </param>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
82 <param name="ori_output" type="boolean" checked="true" label="Keep the original SnpEff output" />
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
83 <param name="stats" type="boolean" checked="true" label="Produce a summary file of results" />
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
84
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
85 <conditional name="snpeff_settings">
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
86 <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.">
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
87 <option value="default">default settings</option>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
88 <option value="change">change settings</option>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
89 </param>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
90 <when value="default">
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
91 ## default settings for SnpEff
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
92 <param name="chr" type="hidden" value=""/>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
93 <param name="min_cov" type="hidden" value=""/>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
94 <param name="min_qual" type="hidden" value=""/>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
95 <param name="no_ds" type="hidden" value=""/>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
96 <param name="no_us" type="hidden" value=""/>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
97 <param name="no_intron" type="hidden" value=""/>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
98 <param name="no_intergenic" type="hidden" value=""/>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
99 <param name="no_utr" type="hidden" value=""/>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
100 <param name="ud" type="hidden" value=""/>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
101 </when>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
102 <when value="change">
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
103 <param name="chr" type="boolean" truevalue="-chr" falsevalue="" checked="false" label="prepend 'chr' to chromosome names, e.g., 'chr7' instead of '7'" />
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
104 <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"/>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
105 <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"/>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
106 <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"/>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
107 <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"/>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
108 <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"/>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
109 <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"/>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
110 <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"/>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
111 <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"/>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
112 </when>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
113 </conditional>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
114 </when>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
115 </conditional>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
116 </inputs>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
117
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
118 <outputs>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
119 <data name="outputfile" format="html" >
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
120 <change_format>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
121 <when input="formatting.oformat" value="text" format="tabular"/>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
122 </change_format>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
123 </data>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
124 <data name="snpeff_file" format="vcf" >
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
125 <filter>(annotool['name']=="snpeff" and annotool['ori_output'])</filter>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
126 </data>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
127 <data name="summary_file" format="html">
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
128 <filter>(annotool['name']=="snpeff" and annotool['stats'])</filter>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
129 </data>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
130 </outputs>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
131
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
132 <help>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
133 .. class:: infomark
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
134
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
135 **What it does**
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
136
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
137 The tool turns a variant list in VCF format into a more readable summary table listing variant sites and effects.
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
138
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
139 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.
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
140
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
141 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.
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
142 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.
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
143
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
144 As output file formats HTML or plain text are supported.
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
145 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.
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
146
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
147 The behavior of this feature depends on:
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
148
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
149 1) Recognition of the species that is analyzed
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
150
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
151 You can declare the species you are working with using the *Species* text field.
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
152 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.
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
153 If no species gets assigned in either way, no hyperlinks will be generated and the html output will look essentially like plain text.
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
154
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
155 2) Available hyperlink formatting rules for this species
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
156
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
157 When the species has been recognized, the tool checks if you have selected an *optional file with hyperlink formatting instructions*.
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
158 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.
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
159 If no matching entry is found in the file, an error will be raised.
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
160
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
161 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.
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
162 If not, no hyperlinks will be generated and the html output will look essentially like plain text.
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
163
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
164 **TIP:**
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
165 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.
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
166
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
167 .. _tell us about the problem: mailto:mimodd@googlegroups.com
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
168 </help>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
169 </tool>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
170