Mercurial > repos > iuc > snpsift

annotate snpSift_extractFields.xml @ 20:f90f08ed9810 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit df8a21df77acffe40c0bc0fe0409ca1b529cd7fc"
author iuc
date Sat, 11 Sep 2021 07:17:20 +0000
parents ede8954f5c82
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1 <tool id="snpSift_extractFields" name="SnpSift Extract Fields" version="@WRAPPER_VERSION@.galaxy0">
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2 <options sanitize="False" />
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3 <description>from a VCF file into a tabular file</description>
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4 <macros>
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5 <import>snpSift_macros.xml</import>
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6 </macros>
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7 <expand macro="requirements" />
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8 <expand macro="stdio" />
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9 <expand macro="version_command" />
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10 <command><![CDATA[
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11 @CONDA_SNPSIFT_JAR_PATH@ &&
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12 cat '${input}'
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13 #if $one_effect_per_line:
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14 | perl "\$SNPSIFT_JAR_PATH/scripts/vcfEffOnePerLine.pl"
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15 #end if
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16 | SnpSift -Xmx6G extractFields
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17 #if $separator:
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18 -s '${separator}'
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19 #end if
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20 #if $empty_text:
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21 -e '${empty_text}'
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22 #end if
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23 -
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24 #echo ' '.join(['"%s"' % x for x in $extract.split()])
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25 > '${output}'
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26 ]]></command>
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27 <inputs>
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28 <param name="input" type="data" format="vcf" label="Variant input file in VCF format"/>
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29 <param name="extract" type="text" label="Fields to extract" value="CHROM POS ID REF ALT FILTER" help="Separated by spaces. See help below for an explanation" />
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30 <param name="one_effect_per_line" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="One effect per line" help="When variants have more than one effect, lists one effect per line, while all other parameters in the line are repeated across mutiple lines" />
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31 <param name="separator" type="text" value="" label="multiple field separator" help="Separate multiple fields in one column with this character, e.g. a comma, rather than a column for each of the multiple values" argument="-s" />
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32 <param name="empty_text" type="text" value="" label="empty field text" help="Represent empty fields with this value, rather than leaving them blank" argument="-e"/>
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33 </inputs>
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34 <outputs>
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35 <data name="output" format="tabular" />
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36 </outputs>
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37 <tests>
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38 <test>
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39 <param name="input" ftype="vcf" value="test_rmInfo.vcf"/>
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40 <param name="extract" value="CHROM POS REF ALT EFF[*].EFFECT"/>
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41 <output name="output">
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42 <assert_contents>
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43 <has_text text="INTRAGENIC" />
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44 <not_has_text text="DOWNSTREAM,INTRAGENIC,INTRON,UTR_3_PRIME" />
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45 </assert_contents>
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46 </output>
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47 </test>
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48 <test>
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49 <param name="input" ftype="vcf" value="test_rmInfo.vcf"/>
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50 <param name="extract" value="CHROM POS REF ALT EFF[*].EFFECT"/>
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51 <param name="separator" value=","/>
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52 <output name="output">
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53 <assert_contents>
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54 <has_text text="DOWNSTREAM,INTRAGENIC,INTRON,UTR_3_PRIME" />
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55 </assert_contents>
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56 </output>
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57 </test>
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58 <test>
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59 <param name="input" ftype="vcf" value="extFields_test3_in.vcf"/>
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60 <param name="extract" value="CHROM POS ID REF ALT FILTER ANN[*].EFFECT"/>
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61 <param name="one_effect_per_line" value="true"/>
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62 <output name="output" value="extFields_test3_out.vcf"/>
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63 </test>
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64 </tests>
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65 <help><![CDATA[
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66 **What is does**
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68 `SnpSift Extract Fields <http://snpeff.sourceforge.net/SnpSift.html#Extract>`_ selects columns from a VCF dataset into a Tab-delimited format.
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69
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70 ------
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71
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72 .. class:: infomark
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74 **How to know which fields to extract?**
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76 A VCF dataset contains mandatory fields as well as optional fields. Mandatory fields are required by `VCF specifications <https://samtools.github.io/hts-specs/VCFv4.2.pdf>`_ and present in any valid VCF dataset. The **Fields to extract** input box of the tool above is already pre-filled with names of mandatory fields.
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77
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78 To know what other fields are available in a given VCF file simply look at its header. `INFO` and `FORMAT` lines will contain description of existing fields. For example, if you see a line:
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80 ##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of samples with data">
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81
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82 you can use *NS* as the field name.
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83
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84 ------
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85
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86 **Dealing with field generated with SnpEff**
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87
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88 The current version of `SnpEff <http://snpeff.sourceforge.net/SnpEff_manual.html>`_ produces so called *ANN* fields::
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89
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90 "ANN[*].ALLELE" (alias GENOTYPE)
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91 "ANN[*].EFFECT" (alias ANNOTATION): Effect in Sequence ontology terms (e.g. 'missense_variant', 'synonymous_variant', 'stop_gained', etc.)
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92 "ANN[*].IMPACT" { HIGH, MODERATE, LOW, MODIFIER }
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93 "ANN[*].GENE" Gene name (e.g. 'PSD3')
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94 "ANN[*].GENEID" Gene ID
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95 "ANN[*].FEATURE"
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96 "ANN[*].FEATUREID" (alias TRID: Transcript ID)
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97 "ANN[*].BIOTYPE" Biotype, as described by the annotations (e.g. 'protein_coding')
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98 "ANN[*].RANK" Exon or Intron rank (i.e. exon number in a transcript)
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99 "ANN[*].HGVS_C" (alias HGVS_DNA, CODON): Variant in HGVS (DNA) notation
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100 "ANN[*].HGVS_P" (alias HGVS, HGVS_PROT, AA): Variant in HGVS (protein) notation
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101 "ANN[*].CDNA_POS" (alias POS_CDNA)
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102 "ANN[*].CDNA_LEN" (alias LEN_CDNA)
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103 "ANN[*].CDS_POS" (alias POS_CDS)
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104 "ANN[*].CDS_LEN" (alias LEN_CDS)
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105 "ANN[*].AA_POS" (alias POS_AA)
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106 "ANN[*].AA_LEN" (alias LEN_AA)
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107 "ANN[*].DISTANCE"
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108 "ANN[*].ERRORS" (alias WARNING, INFOS)
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109
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110 Older versions produced *EFF* fields::
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111
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112 "EFF[*].EFFECT"
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113 "EFF[*].IMPACT"
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114 "EFF[*].FUNCLASS"
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115 "EFF[*].CODON"
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116 "EFF[*].AA"
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117 "EFF[*].AA_LEN"
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118 "EFF[*].GENE"
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119 "EFF[*].BIOTYPE"
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120 "EFF[*].CODING"
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121 "EFF[*].TRID"
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122 "EFF[*].RANK"
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123
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124 In addition there are *LOF* and *NMD* fields::
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125
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126 "LOF[*].GENE"
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127 "LOF[*].GENEID"
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128 "LOF[*].NUMTR"
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129 "LOF[*].PERC"
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130
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131 "NMD[*].GENE"
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132 "NMD[*].GENEID"
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133 "NMD[*].NUMTR"
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134 "NMD[*].PERC"
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135
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136 To find our whether your VCF contains *ANN* or *EFF* annotations simply look at its header.
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137
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138 -----
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139
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140 **Usage examples**
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141
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142 *Extracting chromosome, position, ID and allele frequency from a VCF file*:
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143
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144 **CHROM POS ID AF**
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145
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146 The result will look something like::
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147
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148 #CHROM POS ID AF
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149 1 69134 0.086
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150 1 69496 rs150690004 0.001
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151
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152 *Extracting genotype fields*:
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153
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154 **CHROM POS ID THETA GEN[0].GL[1] GEN[1].GL GEN[3].GL[*] GEN[*].GT**
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155
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156 This means to extract:
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157
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158 - CHROM POS ID: regular fields (as in the previous example)
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159 - THETA : This one is from INFO
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160 - GEN[0].GL[1] : Second likelihood from first genotype
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161 - GEN[1].GL : The whole GL field (all entries without separating them)
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162 - GEN[3].GL[*] : All likelihoods form genotype 3 (this time they will be tab separated, as opposed to the previous one).
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163 - GEN[*].GT : Genotype subfields (GT) from ALL samples (tab separated).
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164
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165 The result will look something like::
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166
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167 #CHROM POS ID THETA GEN[0].GL[1] GEN[1].GL GEN[3].GL[*] GEN[*].GT
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168 1 10583 rs58108140 0.0046 -0.47 -0.24,-0.44,-1.16 -0.48 -0.48 -0.48 0|0 0|0 0|0 0|1 0|0 0|1 0|0 0|0 0|1
ede8954f5c82 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
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169 1 10611 rs189107123 0.0077 -0.48 -0.24,-0.44,-1.16 -0.48 -0.48 -0.48 0|0 0|1 0|0 0|0 0|0 0|0 0|0 0|0 0|0
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170 1 13302 rs180734498 0.0048 -0.58 -2.45,-0.00,-5.00 -0.48 -0.48 -0.48 0|0 0|1 0|0 0|0 0|0 1|0 0|0 0|1 0|0
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171
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172 *Extracting fields with multiple values*:
ede8954f5c82 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
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173 (notice that there are multiple effect columns per line because there are multiple effects per variant)
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174
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175 **CHROM POS REF ALT ANN[*].EFFECT**
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176
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177 The result will look something like::
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178
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179 #CHROM POS REF ALT ANN[*].EFFECT
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180 22 17071756 T C 3_prime_UTR_variant downstream_gene_variant
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181 22 17072035 C T missense_variant downstream_gene_variant
ede8954f5c82 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
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182 22 17072258 C A missense_variant downstream_gene_variant
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183
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184 *Extracting fields with multiple values using a comma as a multiple field separator:*
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185
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186 **CHROM POS REF ALT ANN[*].EFFECT ANN[*].HGVS_P**
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187
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188 The result will look something like::
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189
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190 #CHROM POS REF ALT ANN[*].EFFECT ANN[*].HGVS_P
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191 22 17071756 T C 3_prime_UTR_variant,downstream_gene_variant .,.
ede8954f5c82 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
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192 22 17072035 C T missense_variant,downstream_gene_variant p.Gly469Glu,.
ede8954f5c82 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
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193 22 17072258 C A missense_variant,downstream_gene_variant p.Gly395Cys,.
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194
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195 *Extracting fields with multiple values, one effect per line:*
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196
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197 **CHROM POS REF ALT ANN[*].EFFECT**
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198
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199 The result will look something like::
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200
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201 #CHROM POS REF ALT ANN[*].EFFECT
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202 22 17071756 T C 3_prime_UTR_variant
ede8954f5c82 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
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203 22 17071756 T C downstream_gene_variant
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204 22 17072035 C T missense_variant
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205 22 17072035 C T downstream_gene_variant
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206 22 17072258 C A missense_variant
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207 22 17072258 C A downstream_gene_variant
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208
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209 @EXTERNAL_DOCUMENTATION@
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210 - http://snpeff.sourceforge.net/SnpSift.html#Extract
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211 ]]></help>
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212 <expand macro="citations" />
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213 </tool>