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comparison annotate_variants.xml @ 23:5db0545b9004 draft

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update to v0.1.7.3
author wolma
date Thu, 21 Jul 2016 03:55:49 -0400
parents c46406466625
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22:24154c580718 23:5db0545b9004
1 <tool id="annotate_variants" name="Variant Annotation" version="0.1.7.2"> 1 <tool id="annotate_variants" name="Variant Annotation" version="0.1.7.3">
2 <description>Predict the effects of SNPs and indels on known genes in the reference genome using SnpEff</description> 2 <description>Predict the effects of SNPs and indels on known genes in the reference genome using SnpEff</description>
3 <macros> 3 <macros>
4 <import>toolshed_macros.xml</import> 4 <import>toolshed_macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements" />
7 <version_command>python3 -m MiModD version -q</version_command> 7 <version_command>python3 -m MiModD version -q</version_command>
8 <command> 8 <command>
9 python3 -m MiModD annotate 9 python3 -m MiModD annotate
10 10
11 "$inputfile" 11 "$inputfile"
48 #end if 48 #end if
49 --verbose 49 --verbose
50 </command> 50 </command>
51 51
52 <inputs> 52 <inputs>
53 <param name="inputfile" type="data" format="vcf" label="vcf inputfile to be annotated" /> 53 <param format="vcf" label="vcf inputfile to be annotated" name="inputfile" type="data" />
54 <param name="grouping" type="select" label="Group variants by"> 54 <param label="Group variants by" name="grouping" type="select">
55 <option value="">order in the input file</option> 55 <option value="">order in the input file</option>
56 <option value="by_sample">sample</option> 56 <option value="by_sample">sample</option>
57 <option value="by_genes">most affected genes</option> 57 <option value="by_genes">most affected genes</option>
58 </param> 58 </param>
59 <conditional name="formatting"> 59 <conditional name="formatting">
60 <param name="oformat" type="select" label="Format of the annotation output file"> 60 <param label="Format of the annotation output file" name="oformat" type="select">
61 <option value="html">HTML</option> 61 <option value="html">HTML</option>
62 <option value="text">Tab-separated plain text</option> 62 <option value="text">Tab-separated plain text</option>
63 </param> 63 </param>
64 <when value="html"> 64 <when value="html">
65 <param name="formatter_file" type="data" format="txt" optional="true" label="Optional file with hyperlink formatting instructions" /> 65 <param format="txt" label="Optional file with hyperlink formatting instructions" name="formatter_file" optional="true" type="data" />
66 <param name="species" type="text" label="Species" help="Overwrite the species guess from the SnpEff genome, often not necessary" /> 66 <param help="Overwrite the species guess from the SnpEff genome, often not necessary" label="Species" name="species" type="text" />
67 </when> 67 </when>
68 </conditional> 68 </conditional>
69 <conditional name="annotool"> 69 <conditional name="annotool">
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."> 70 <param 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." label="Use this tool to annotate the input file" name="name" type="select">
71 <option value="snpeff">SnpEff</option> 71 <option value="snpeff">SnpEff</option>
72 <option value="None">None</option> 72 <option value="None">None</option>
73 </param> 73 </param>
74 <when value="snpeff"> 74 <when value="snpeff">
75 <param name="genome_list" type="data" format="tabular" label="genome list" /> 75 <param format="tabular" label="genome list" name="genome_list" type="data" />
76 <param name="genomeVersion" type="select" label="Genome"> 76 <param label="Genome" name="genomeVersion" type="select">
77 <options from_dataset="genome_list"> 77 <options from_dataset="genome_list">
78 <column name="name" index="0"/> 78 <column index="0" name="name" />
79 <column name="value" index="1"/> 79 <column index="1" name="value" />
80 </options> 80 </options>
81 </param> 81 </param>
82 <param name="ori_output" type="boolean" checked="true" label="Keep the original SnpEff output" /> 82 <param checked="true" label="Keep the original SnpEff output" name="ori_output" type="boolean" />
83 <param name="stats" type="boolean" checked="true" label="Produce a summary file of results" /> 83 <param checked="true" label="Produce a summary file of results" name="stats" type="boolean" />
84 84
85 <conditional name="snpeff_settings"> 85 <conditional name="snpeff_settings">
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."> 86 <param help="This section lets you specify the detailed parameter settings for the SnpEff tool." label="SnpEff-specific parameter settings" name="detail_level" type="select">
87 <option value="default">default settings</option> 87 <option value="default">default settings</option>
88 <option value="change">change settings</option> 88 <option value="change">change settings</option>
89 </param> 89 </param>
90 <when value="default"> 90 <when value="default">
91 ## default settings for SnpEff 91 ## default settings for SnpEff
92 <param name="chr" type="hidden" value=""/> 92 <param name="chr" type="hidden" value="" />
93 <param name="min_cov" type="hidden" value=""/> 93 <param name="min_cov" type="hidden" value="" />
94 <param name="min_qual" type="hidden" value=""/> 94 <param name="min_qual" type="hidden" value="" />
95 <param name="no_ds" type="hidden" value=""/> 95 <param name="no_ds" type="hidden" value="" />
96 <param name="no_us" type="hidden" value=""/> 96 <param name="no_us" type="hidden" value="" />
97 <param name="no_intron" type="hidden" value=""/> 97 <param name="no_intron" type="hidden" value="" />
98 <param name="no_intergenic" type="hidden" value=""/> 98 <param name="no_intergenic" type="hidden" value="" />
99 <param name="no_utr" type="hidden" value=""/> 99 <param name="no_utr" type="hidden" value="" />
100 <param name="ud" type="hidden" value=""/> 100 <param name="ud" type="hidden" value="" />
101 </when> 101 </when>
102 <when value="change"> 102 <when value="change">
103 <param name="chr" type="boolean" truevalue="-chr" falsevalue="" checked="false" label="prepend 'chr' to chromosome names, e.g., 'chr7' instead of '7'" /> 103 <param checked="false" falsevalue="" label="prepend 'chr' to chromosome names, e.g., 'chr7' instead of '7'" name="chr" truevalue="-chr" type="boolean" />
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"/> 104 <param help="do not include variants with a coverage lower than this value" label="minimum coverage (default = not used)" name="min_cov" optional="true" type="integer" />
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"/> 105 <param help="do not include variants with a quality lower than this value" label="minimum quality (default = not used)" name="min_qual" optional="true" type="integer" />
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"/> 106 <param checked="false" falsevalue="" help="annotation of effects on the downstream region of genes can be suppressed" label="do not show downstream changes" name="no_ds" truevalue="--no-downstream" type="boolean" />
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"/> 107 <param checked="false" falsevalue="" help="annotation of effects on the upstream region of genes can be suppressed" label="do not show upstream changes" name="no_us" truevalue="--no-upstream" type="boolean" />
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"/> 108 <param checked="false" falsevalue="" help="annotation of effects on introns of genes can be suppressed" label="do not show intron changes" name="no_intron" truevalue="--no-intron" type="boolean" />
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"/> 109 <param checked="false" falsevalue="" help="annotation of effects on intergenic regions can be suppressed" label="do not show intergenic changes" name="no_intergenic" truevalue="--no-intergenic" type="boolean" />
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"/> 110 <param checked="false" falsevalue="" help="annotation of effects on the untranslated regions of genes can be suppressed" label="do not show UTR changes" name="no_utr" truevalue="--no-utr" type="boolean" />
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"/> 111 <param help="specify the upstream/downstream interval length, i.e., variants more than INTERVAL nts from the next annotated gene are considered to be intergenic" label="upstream downstream interval length (default = 5000 bases)" name="ud" optional="true" type="integer" />
112 </when> 112 </when>
113 </conditional> 113 </conditional>
114 </when> 114 </when>
115 </conditional> 115 </conditional>
116 </inputs> 116 </inputs>
117 117
118 <outputs> 118 <outputs>
119 <data name="outputfile" format="html" > 119 <data format="html" name="outputfile">
120 <change_format> 120 <change_format>
121 <when input="formatting.oformat" value="text" format="tabular"/> 121 <when format="tabular" input="formatting.oformat" value="text" />
122 </change_format> 122 </change_format>
123 </data> 123 </data>
124 <data name="snpeff_file" format="vcf" > 124 <data format="vcf" name="snpeff_file">
125 <filter>(annotool['name']=="snpeff" and annotool['ori_output'])</filter> 125 <filter>(annotool['name']=="snpeff" and annotool['ori_output'])</filter>
126 </data> 126 </data>
127 <data name="summary_file" format="html"> 127 <data format="html" name="summary_file">
128 <filter>(annotool['name']=="snpeff" and annotool['stats'])</filter> 128 <filter>(annotool['name']=="snpeff" and annotool['stats'])</filter>
129 </data> 129 </data>
130 </outputs> 130 </outputs>
131 131
132 <help> 132 <help>
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. 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.
166 166
167 .. _tell us about the problem: mailto:mimodd@googlegroups.com 167 .. _tell us about the problem: mailto:mimodd@googlegroups.com
168 </help> 168 </help>
169 </tool> 169 </tool>
170