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1 <tool id="hgv_sift" name="SIFT" version="1.0.0">
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2 <description>predictions of functional sites</description>
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3
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4 <command interpreter="bash">
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5 sift_variants_wrapper.sh "$input" "$output" "${input.metadata.dbkey}" "${GALAXY_DATA_INDEX_DIR}/sift_db.loc" "$chrom_col" "$pos_col" "$base" "$allele_col" "$strand_source.strand_col" "$comment_source.comment_col" "$output_opts"
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6 </command>
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7
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8 <inputs>
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9 <param name="input" type="data" format="tabular" label="Dataset">
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10 <validator type="unspecified_build"/>
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11 <validator type="dataset_metadata_in_file" filename="sift_db.loc" metadata_name="dbkey" metadata_column="0" message="Data is currently not available for the specified build."/>
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12 </param>
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13 <param name="chrom_col" type="data_column" data_ref="input" label="Column with chromosome"/>
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14 <param name="pos_col" type="data_column" data_ref="input" numerical="true" label="Column with position"/>
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15 <param name="base" type="select" label="Position coordinates are">
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16 <option value="1" selected="true">one-based</option>
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17 <option value="0">zero-based</option>
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18 </param>
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19 <param name="allele_col" type="data_column" data_ref="input" label="Column with allele"/>
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20 <conditional name="strand_source">
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21 <param name="strand_choice" type="select" label="Strand info">
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22 <option value="data_column" selected="true">a column in the dataset</option>
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23 <option value="all_pos">all on sense/forward/+ strand</option>
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24 <option value="all_neg">all on antisense/reverse/- strand</option>
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25 </param>
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26 <when value="data_column">
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27 <param name="strand_col" type="data_column" data_ref="input" label="Column with strand"/>
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28 </when>
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29 <when value="all_pos">
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30 <param name="strand_col" type="hidden" value="+"/>
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31 </when>
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32 <when value="all_neg">
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33 <param name="strand_col" type="hidden" value="-"/>
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34 </when>
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35 </conditional>
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36 <conditional name="comment_source">
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37 <param name="comment_choice" type="select" label="Include comment column">
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38 <option value="no" selected="true">no</option>
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39 <option value="yes">yes</option>
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40 </param>
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41 <when value="no">
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42 <param name="comment_col" type="hidden" value="-"/>
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43 </when>
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44 <when value="yes">
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45 <param name="comment_col" type="data_column" data_ref="input" label="Column with comment"/>
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46 </when>
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47 </conditional>
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48 <param name="output_opts" type="select" multiple="true" display="checkboxes" label="Include the following additional fields in the output">
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49 <option value="A">Ensembl Gene ID</option>
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50 <option value="B">Gene Name</option>
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51 <option value="C">Gene Description</option>
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52 <option value="D">Ensembl Protein Family ID</option>
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53 <option value="E">Ensembl Protein Family Description</option>
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54 <option value="F">Ensembl Transcript Status (Known / Novel)</option>
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55 <option value="G">Protein Family Size</option>
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56 <option value="H">Ka/Ks (Human-mouse)</option>
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57 <option value="I">Ka/Ks (Human-macaque)</option>
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58 <option value="J">OMIM Disease</option>
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59 <option value="K">Allele Frequencies (All Hapmap Populations - weighted average)</option>
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60 <option value="L">Allele Frequencies (CEU Hapmap population)</option>
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61 </param>
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62 </inputs>
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63
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64 <outputs>
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65 <data format="tabular" name="output" />
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66 </outputs>
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67
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68 <requirements>
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69 <requirement type="binary">awk</requirement>
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70 <requirement type="binary">rm</requirement>
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71 <requirement type="binary">sed</requirement>
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72 </requirements>
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73
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74 <tests>
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75 <test>
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76 <param name="input" value="sift_variants.tab" ftype="tabular" dbkey="hg18"/>
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77 <param name="chrom_col" value="1"/>
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78 <param name="pos_col" value="3"/>
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79 <param name="base" value="1"/>
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80 <param name="allele_col" value="5"/>
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81 <param name="strand_choice" value="data_column"/>
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82 <param name="strand_col" value="4"/>
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83 <param name="output_opts" value="A"/>
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84 <output name="output" file="sift_variants_result.tab"/>
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85 </test>
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86 </tests>
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87
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88 <help>
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89 .. class:: warningmark
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90
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91 This currently works only for builds hg18 or hg19.
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92
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93 -----
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94
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95 **Dataset formats**
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96
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97 The input and output datasets are tabular_.
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98 (`Dataset missing?`_)
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99
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100 .. _tabular: ./static/formatHelp.html#tab
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101 .. _Dataset missing?: ./static/formatHelp.html
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102
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103 -----
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104
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105 **What it does**
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106
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107 SIFT predicts whether an amino-acid substitution affects protein function,
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108 based on sequence homology and the physical properties of amino acids.
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109 SIFT can be applied to naturally occurring non-synonymous polymorphisms
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110 and laboratory-induced missense mutations. This tool uses SQLite databases
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111 containing pre-computed SIFT scores and annotations for all possible nucleotide
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112 substitutions at each position in the human exome. Allele frequency data
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113 are from the HapMap frequency database, and additional transcript and
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114 gene-level data are from Ensembl BioMart.
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115
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116 The input dataset must contain columns for the chromosome, position, and
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117 alleles. The alleles must be two nucleotides separated by '/',
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118 usually the reference allele and the allele of interest.
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119 The strand must either be in another column or all the same.
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120 The output contains a standard set of columns plus the additional ones that
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121 have been selected from the list above.
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122
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123 Website: http://sift.jcvi.org/
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124
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125 -----
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126
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127 **Example**
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128
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129 - input file::
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130
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131 chr3 81780820 + T/C
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132 chr2 230341630 + G/A
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133 chr2 43881517 + A/T
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134 chr2 43857514 + T/C
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135 chr6 88375602 + G/A
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136 chr22 29307353 - T/A
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137 chr10 115912482 - G/T
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138 chr10 115900918 - C/T
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139 chr16 69875502 + G/T
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140 etc.
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141
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142 - output file::
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143
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144 #Chrom Position Strand Allele Codons Transcript ID Protein ID Substitution Region dbSNP ID SNP Type Prediction Score Median Info Num seqs at position User Comment
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145 chr3 81780820 + T/C AGA-gGA ENST00000264326 ENSP00000264326 R190G EXON CDS rs2229519:C Nonsynonymous DAMAGING 0.04 3.06 149
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146 chr2 230341630 + G/T - ENST00000389045 ENSP00000373697 NA EXON CDS rs1803846:A Unknown Not scored NA NA NA
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147 chr2 43881517 + A/T ATA-tTA ENST00000260605 ENSP00000260605 I230L EXON CDS rs11556157:T Nonsynonymous TOLERATED 0.47 3.19 7
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148 chr2 43857514 + T/C TTT-TcT ENST00000260605 ENSP00000260605 F33S EXON CDS rs2288709:C Nonsynonymous TOLERATED 0.61 3.33 6
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149 chr6 88375602 + G/A GTT-aTT ENST00000257789 ENSP00000257789 V217I EXON CDS rs2307389:A Nonsynonymous TOLERATED 0.75 3.17 13
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150 chr22 29307353 + T/A ACC-tCC ENST00000335214 ENSP00000334612 T264S EXON CDS rs42942:A Nonsynonymous TOLERATED 0.4 3.14 23
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151 chr10 115912482 + C/A CGA-CtA ENST00000369285 ENSP00000358291 R179L EXON CDS rs12782946:T Nonsynonymous TOLERATED 0.06 4.32 2
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152 chr10 115900918 + G/A CAA-tAA ENST00000369287 ENSP00000358293 Q271* EXON CDS rs7095762:T Nonsynonymous N/A N/A N/A N/A
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153 chr16 69875502 + G/T ACA-AaA ENST00000338099 ENSP00000337512 T608K EXON CDS rs3096381:T Nonsynonymous TOLERATED 0.12 3.41 3
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154 etc.
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155
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156 -----
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157
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158 **References**
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159
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160 Ng PC, Henikoff S. (2001) Predicting deleterious amino acid substitutions.
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161 Genome Res. 11(5):863-74.
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162
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163 Ng PC, Henikoff S. (2002) Accounting for human polymorphisms predicted to affect protein function.
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164 Genome Res. 12(3):436-46.
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165
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166 Ng PC, Henikoff S. (2003) SIFT: Predicting amino acid changes that affect protein function.
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167 Nucleic Acids Res. 31(13):3812-4.
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168
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169 Kumar P, Henikoff S, Ng PC. (2009) Predicting the effects of coding non-synonymous variants
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170 on protein function using the SIFT algorithm.
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171 Nat Protoc. 4(7):1073-81. Epub 2009 Jun 25.
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172
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173 </help>
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174 </tool>
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