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1 <tool id="Annovar" name="ANNOVAR" version="2013aug">
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2 <description> Annotate a file using ANNOVAR </description>
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3
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4 <requirements>
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1
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5 <requirement type="package" version="1.7">cgatools</requirement>
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0
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6 </requirements>
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7
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8 <command interpreter="bash">
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9 annovar.sh
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10 --impactscores ${impactscores}
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11 --esp ${esp}
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12 --gerp ${gerp}
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13 --cosmic61 ${cosmic61}
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14 --cosmic63 ${cosmic63}
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15 --cosmic64 ${cosmic64}
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16 --cosmic65 ${cosmic65}
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17 --outall ${annotated}
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18 --outinvalid ${invalid}
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19 --dorunannovar ${dorun}
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20 --inputfile ${infile}
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21 --buildver ${reference.fields.dbkey}
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22 --humandb ${reference.fields.ANNOVAR_humandb}
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23 --scriptsdir ${reference.fields.ANNOVAR_scripts}
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24 --verdbsnp ${verdbsnp}
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25 --geneanno ${geneanno}
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26 --tfbs ${tfbs}
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27 --mce ${mce}
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28 --cytoband ${cytoband}
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29 --segdup ${segdup}
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30 --dgv ${dgv}
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31 --gwas ${gwas}
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32 #if $filetype.type == "other"
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33 --varfile N
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34 --VCF N
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35 --chrcol ${filetype.col_chr}
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36 --startcol ${filetype.col_start}
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37 --endcol ${filetype.col_end}
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38 --obscol ${filetype.col_obs}
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39 --refcol ${filetype.col_ref}
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40
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41 #if $filetype.convertcoords.convert == "Y"
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42 --vartypecol ${filetype.convertcoords.col_vartype}
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43 --convertcoords Y
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44 #else
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45 --convertcoords N
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46 #end if
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47 #end if
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48 #if $filetype.type == "vcf"
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49 --varfile N
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50 --VCF Y
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51 --convertcoords N
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52 #end if
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53 #if $filetype.type == "varfile"
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54 --varfile Y
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55 --VCF N
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56 #end if
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57 --cg46 ${cgfortysix}
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58 --cg69 ${cgsixtynine}
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59 --ver1000g ${ver1000g}
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60
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61 </command>
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62
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63 <inputs>
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64 <param name="dorun" type="hidden" value="Y"/> <!-- will add tool in future to filter on annovar columns, then will call annovar.sh with dorun==N -->
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65 <param name="reference" type="select" label="Reference">
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66 <options from_data_table="annovar_loc" />
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67 </param>
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68
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69 <param name="infile" type="data" label="Select file to annotate" help="Must be CG varfile or a tab-separated file with a 1 line header"/>
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70 <conditional name="filetype">
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71 <param name="type" type="select" label="Select filetype" >
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72 <option value="vcf" selected="false"> VCF4 file </option>
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73 <option value="varfile" selected="false"> CG varfile </option>
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74 <option value="other" selected="false"> Other </option>
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75 </param>
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76 <when value="other">
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77 <param name="col_chr" type="data_column" data_ref="infile" multiple="False" label="Chromosome Column" />
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78 <param name="col_start" type="data_column" data_ref="infile" multiple="False" label="Start Column" />
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79 <param name="col_end" type="data_column" data_ref="infile" multiple="False" label="End Column" />
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80 <param name="col_ref" type="data_column" data_ref="infile" multiple="False" label="Reference Allele Column" />
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81 <param name="col_obs" type="data_column" data_ref="infile" multiple="False" label="Observed Allele Column" />
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82 <conditional name="convertcoords">
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83 <param name="convert" type="select" label="Is this file using Complete Genomics (0-based half-open) cooridinates?" >
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84 <option value="Y"> Yes </option>
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85 <option value="N" selected="True"> No </option>
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86 </param>
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87 <when value="Y">
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88 <param name="col_vartype" type="data_column" data_ref="infile" multiple="False" label="varType Column" />
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89 </when>
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90 </conditional>
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91 </when>
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92 </conditional>
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93
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94
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95
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96 <param name="geneanno" type="select" label="Select Gene Annotation(s)" multiple="true" optional="true" display="checkboxes">
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97 <option value="refSeq" selected="true" > RefSeq </option>
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98 <option value="knowngene"> UCSC KnownGene </option>
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99 <option value="ensgene" > Ensembl </option>
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100 </param>
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101
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102
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103 <!-- region-based annotation -->
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104 <param name="cytoband" type="boolean" checked="False" truevalue="Y" falsevalue="N" label="Cytogenic band Annotation?" help="This option identifies Giemsa-stained chromosomes bands, (e.g. 1q21.1-q23.3)."/>
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105 <param name="tfbs" type="boolean" checked="False" truevalue="Y" falsevalue="N" label="Transcription Factor Binding Site Annotation?"/>
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106 <param name="mce" type="boolean" checked="False" truevalue="Y" falsevalue="N" label="Most Conserved Elements Annotation?" help="This option phastCons 44-way alignments to annotate variants that fall within conserved genomic regions."/>
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107 <param name="segdup" type="boolean" checked="False" truevalue="Y" falsevalue="N" label="Segmental Duplication Annotation?" help="Genetic variants that are mapped to segmental duplications are most likely sequence alignment errors and should be treated with extreme caution."/>
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108 <param name="dgv" type="boolean" checked="False" truevalue="Y" falsevalue="N" label="DGV (Database of Genomic Variants) Annotation?" help="Identify previously reported structural variants in DGV (Database of Genomic Variants) "/>
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109 <param name="gwas" type="boolean" checked="False" truevalue="Y" falsevalue="N" label="GWAS studies Annotation?" help="Identify variants reported in previously published GWAS (Genome-wide association studies) "/>
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110
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111
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112
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113 <!-- filter-based annotation -->
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114 <param name="verdbsnp" type="select" label="Select dbSNP version(s) to annotate with" multiple="true" display="checkboxes" optional="true" help="SNPs in dbSNP may be flagged as Clinically Associated, Select the NonFlagged version if you do not wish to annotate with these SNPs ">
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115 <option value="snp128" > 128 (hg18/hg19) </option>
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116 <option value="snp128NonFlagged"> 128 NonFlagged </option>
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117 <option value="snp129" > 129 (hg18/hg19) </option>
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118 <option value="snp129NonFlagged"> 129 NonFlagged </option>
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119 <option value="snp130" > 130 (hg18/hg19) </option>
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120 <option value="snp130NonFlagged"> 130 NonFlagged </option>
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121 <option value="snp131" > 131 (hg18/hg19) </option>
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122 <option value="snp131NonFlagged"> 131 NonFlagged </option>
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123 <option value="snp132" > 132 (hg18/hg19) </option>
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124 <option value="snp132NonFlagged"> 132 NonFlagged </option>
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125 <option value="snp135" > 135 (hg19 only) </option>
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126 <option value="snp135NonFlagged"> 135 NonFlagged </option>
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127 <option value="snp137" > 137 (hg19 only) </option>
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128 <option value="snp137NonFlagged"> 137 NonFlagged </option>
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129 </param>
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130
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131 <param name="ver1000g" type="select" label="Select 1000Genomes Annotation(s)" multiple="true" display="checkboxes" optional="true" help="2012april database for ALL populations was converted to hg18 using the UCSC liftover program">
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132 <option value="1000g2012apr"> 2012apr (hg18/hg19) (5 populations: AMR,AFR,ASN,CEU,ALL) </option>
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133 <option value="1000g2012feb"> 2012feb (hg19) (1 population: ALL) </option>
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134 <option value="1000g2010nov"> 2010nov (hg19) (1 population: ALL) </option>
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135 <option value="1000g2010jul"> 2010jul (hg18) (4 populations: YRI,JPT,CHB,CEU)</option>
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136 </param>
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137 <!--
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138 <param name="g1000" type="boolean" checked="True" truevalue="Y" falsevalue="N" label="Annotate with 1000genomes project? (version 2012april)"/>
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139 -->
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140
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141
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142 <param name="esp" type="select" label="Select Exome Variant Server version(s) to annotate with" multiple="true" display="checkboxes" optional="true" help="si versions of databases contain indels and chrY calls">
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143 <option value="esp6500si_all" > ESP6500si ALL </option>
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144 <option value="esp6500si_ea" > ESP6500si European Americans </option>
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145 <option value="esp6500si_aa" > ESP6500si African Americans </option>
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146 <option value="esp6500_all" > ESP6500 ALL </option>
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147 <option value="esp6500_ea" > ESP6500 European Americans </option>
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148 <option value="esp6500_aa" > ESP6500 African Americans </option>
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149 <option value="esp5400_all" > ESP5400 ALL </option>
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150 <option value="esp5400_ea" > ESP5400 European Americans </option>
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151 <option value="esp5400_aa" > ESP5400 African Americans </option>
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152 </param>
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153
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154
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155 <param name="gerp" type="boolean" checked="False" truevalue="Y" falsevalue="N" label="GERP++ Annotation?" help="GERP identifies constrained elements in multiple alignments by quantifying substitution deficits (see http://mendel.stanford.edu/SidowLab/downloads/gerp/ for details) This option annotates those variants having GERP++>2 in human genome, as this threshold is typically regarded as evolutionarily conserved and potentially functional"/>
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156
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157 <param name="cgfortysix" type="boolean" checked="False" truevalue="Y" falsevalue="N" label="Complete Genomics 46 Genomes?" help="Diversity Panel; 46 unrelated individuals"/>
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158 <param name="cgsixtynine" type="boolean" checked="False" truevalue="Y" falsevalue="N" label="Complete Genomics 69 Genomes?" help="Diversity Panel, Pedigree, YRI trio and PUR trio"/>
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159 <param name="cosmic61" type="boolean" checked="False" truevalue="Y" falsevalue="N" label="Annotate with COSMIC61? (hg19 only)"/>
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160 <param name="cosmic63" type="boolean" checked="False" truevalue="Y" falsevalue="N" label="Annotate with COSMIC63? (hg19 only)"/>
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161 <param name="cosmic64" type="boolean" checked="False" truevalue="Y" falsevalue="N" label="Annotate with COSMIC64? (hg19 only)"/>
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162 <param name="cosmic65" type="boolean" checked="False" truevalue="Y" falsevalue="N" label="Annotate with COSMIC65? (hg19 only)"/>
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163
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164 <param name="impactscores" type="select" label="Select functional impact scores annotate with" multiple="true" display="checkboxes" optional="true" help="LJB refers to Liu, Jian, Boerwinkle paper in Human Mutation, pubmed ID 21520341.">
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165 <option value="avsift"> AV SIFT </option>
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166 <option value="ljbsift"> LJB SIFT (corresponds to 1-SIFT)</option>
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167 <option value="pp2"> PolyPhen2 </option>
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168 <option value="mutationtaster" > MutationTaster </option>
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169 <option value="lrt"> LRT (Likelihood Ratio Test) </option>
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170 <option value="phylop"> PhyloP </option>
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171 </param>
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172
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173
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174 <!-- prefix for output file so you dont have to manually rename history items -->
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175 <param name="fname" type="text" value="" label="Prefix for your output file" help="Optional"/>
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176
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177 </inputs>
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178
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179 <outputs>
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180 <data format="tabular" name="invalid" label="$fname ANNOVAR Invalid input on ${on_string}"/>
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181 <data format="tabular" name="annotated" label="$fname ANNOVAR Annotated variants on ${on_string}"/>
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182 </outputs>
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183
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184 <help>
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185 **What it does**
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186
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187 This tool will annotate a file using ANNOVAR.
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188
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189 **ANNOVAR Website and Documentation**
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190
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191 Website: http://www.openbioinformatics.org/annovar/
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192
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193 Paper: http://nar.oxfordjournals.org/content/38/16/e164
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194
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195 **Input Formats**
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196
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197 Input Formats may be one of the following:
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198
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199 VCF file
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200
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201 Complete Genomics varfile
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202
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203 Custom tab-delimited file (specify chromosome, start, end, reference allele, observed allele columns)
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204
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205 Custom tab-delimited CG-derived file (specify chromosome, start, end, reference allele, observed allele, varType columns)
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206
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207 </help>
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208
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209 </tool>
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210
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211
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