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comparison annotate_variants.xml @ 0:6231ae8f87b8

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author wolma
date Wed, 11 Feb 2015 08:29:02 -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 <version_command>mimodd version -q</version_command>
4 <command>
5 mimodd annotate
6
7 "$inputfile"
8
9 #if $str($annotool.name)=='snpeff':
10 --genome "${annotool.genomeVersion}"
11 #if $annotool.ori_output:
12 --snpeff-out "$snpeff_file"
13 #end if
14 #if $annotool.stats:
15 --stats "$summary_file"
16 #end if
17 ${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}
18 #if $annotool.snpeff_settings.min_cov:
19 --minC "${annotool.snpeff_settings.min_cov}"
20 #end if
21 #if $annotool.snpeff_settings.min_qual:
22 --minQ "${annotool.snpeff_settings.min_qual}"
23 #end if
24 #if $annotool.snpeff_settings.ud:
25 --ud "${annotool.snpeff_settings.ud}"
26 #end if
27 #end if
28
29 --ofile "$outputfile"
30 #if $str($formatting.oformat) == "text":
31 --oformat text
32 #end if
33 #if $str($formatting.oformat) == "html":
34 #if $formatting.formatter_file:
35 --link "${formatting.formatter_file}"
36 #end if
37 #if $formatting.species
38 --species "${formatting.species}"
39 #end if
40 #end if
41
42 #if $str($grouping):
43 --grouping $grouping
44 #end if
45 --verbose
46 </command>
47
48 <inputs>
49 <param name="inputfile" type="data" format="vcf" label="vcf inputfile to be annotated" />
50 <param name="grouping" type="select" label="Group variants by">
51 <option value="">order in the input file</option>
52 <option value="by_sample">sample</option>
53 <option value="by_genes">most affected genes</option>
54 </param>
55 <conditional name="formatting">
56 <param name="oformat" type="select" label="Format of the annotation output file">
57 <option value="html">HTML</option>
58 <option value="text">Tab-separated plain text</option>
59 </param>
60 <when value="html">
61 <param name="formatter_file" type="data" format="txt" optional="true" label="Optional file with hyperlink formatting instructions" />
62 <param name="species" type="text" label="Species" help="Overwrite the species guess from the SnpEff genome, often not necessary" />
63 </when>
64 </conditional>
65 <conditional name="annotool">
66 <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.">
67 <option value="snpeff">SnpEff</option>
68 <option value="None">None</option>
69 </param>
70 <when value="snpeff">
71 <param name="genome_list" type="data" format="tabular" label="genome list" />
72 <param name="genomeVersion" type="select" label="Genome">
73 <options from_dataset="genome_list">
74 <column name="name" index="0"/>
75 <column name="value" index="1"/>
76 </options>
77 </param>
78 <param name="ori_output" type="boolean" checked="true" label="Keep the original SnpEff output" />
79 <param name="stats" type="boolean" checked="true" label="Produce a summary file of results" />
80
81 <conditional name="snpeff_settings">
82 <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.">
83 <option value="default">default settings</option>
84 <option value="change">change settings</option>
85 </param>
86 <when value="default">
87 ## default settings for SnpEff
88 <param name="chr" type="hidden" value=""/>
89 <param name="min_cov" type="hidden" value=""/>
90 <param name="min_qual" type="hidden" value=""/>
91 <param name="no_ds" type="hidden" value=""/>
92 <param name="no_us" type="hidden" value=""/>
93 <param name="no_intron" type="hidden" value=""/>
94 <param name="no_intergenic" type="hidden" value=""/>
95 <param name="no_utr" type="hidden" value=""/>
96 <param name="ud" type="hidden" value=""/>
97 </when>
98 <when value="change">
99 <param name="chr" type="boolean" truevalue="-chr" falsevalue="" checked="false" label="prepend 'chr' to chromosome names, e.g., 'chr7' instead of '7'" />
100 <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"/>
101 <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"/>
102 <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"/>
103 <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"/>
104 <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"/>
105 <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"/>
106 <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"/>
107 <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"/>
108 </when>
109 </conditional>
110 </when>
111 </conditional>
112 </inputs>
113
114 <outputs>
115 <data name="outputfile" format="html" >
116 <change_format>
117 <when input="formatting.oformat" value="text" format="tabular"/>
118 </change_format>
119 </data>
120 <data name="snpeff_file" format="vcf" >
121 <filter>(annotool['name']=="snpeff" and annotool['ori_output'])</filter>
122 </data>
123 <data name="summary_file" format="html">
124 <filter>(annotool['name']=="snpeff" and annotool['stats'])</filter>
125 </data>
126 </outputs>
127
128 <help>
129 .. class:: infomark
130
131 **What it does**
132
133 The tool turns a variant list in VCF format into a more readable summary table listing variant sites and effects.
134
135 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.
136
137 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.
138 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.
139
140 As output file formats HTML or plain text are supported.
141 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.
142
143 The behavior of this feature depends on:
144
145 1) Recognition of the species that is analyzed
146
147 You can declare the species you are working with using the *Species* text field.
148 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.
149 If no species gets assigned in either way, no hyperlinks will be generated and the html output will look essentially like plain text.
150
151 2) Available hyperlink formatting rules for this species
152
153 When the species has been recognized, the tool checks if you have selected an *optional file with hyperlink formatting instructions*.
154 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.
155 If no matching entry is found in the file, an error will be raised.
156
157 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.
158 If not, no hyperlinks will be generated and the html output will look essentially like plain text.
159
160 **TIP:**
161 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.
162
163 .. _tell us about the problem: mailto:mimodd@googlegroups.com
164 </help>
165 </tool>
166