Mercurial > repos > iuc > snpsift

annotate snpSift_extractFields.xml @ 14:80da7fae14b8 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f
author iuc
date Mon, 05 Dec 2016 12:10:54 -0500
parents ed810da439cc
children 8bd645802765
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1 <tool id="snpSift_extractFields" name="SnpSift Extract Fields" version="@WRAPPER_VERSION@.1">
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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 | "\$SNPSIFT_JAR_PATH/scripts/vcfEffOnePerLine.pl"
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15 #end if
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16 | java -Xmx6G -jar "\$SNPSIFT_JAR_PATH/SnpSift.jar" 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 ]]>
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27 </command>
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28 <inputs>
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29 <param format="vcf" name="input" type="data" label="Variant input file in VCF format"/>
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30 <param name="extract" type="text" label="Extract" help="Need help? See below a few examples." />
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31 <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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32 <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" />
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33 <param name="empty_text" type="text" value="" label="empty field text" help="Represent empty fields with this value, rather than leaving them blank" />
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34 </inputs>
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35 <outputs>
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36 <data format="tabular" name="output" />
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37 </outputs>
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38 <tests>
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39 <test>
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40 <param name="input" ftype="vcf" value="test_rmInfo.vcf"/>
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41 <param name="extract" value="CHROM POS REF ALT EFF[*].EFFECT"/>
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42 <output name="output">
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43 <assert_contents>
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44 <has_text text="INTRAGENIC" />
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45 <not_has_text text="DOWNSTREAM,INTRAGENIC,INTRON,UTR_3_PRIME" />
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46 </assert_contents>
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47 </output>
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48 </test>
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49
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50 <test>
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51 <param name="input" ftype="vcf" value="test_rmInfo.vcf"/>
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52 <param name="extract" value="CHROM POS REF ALT EFF[*].EFFECT"/>
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53 <param name="separator" value=","/>
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54 <output name="output">
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55 <assert_contents>
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56 <has_text text="DOWNSTREAM,INTRAGENIC,INTRON,UTR_3_PRIME" />
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57 </assert_contents>
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58 </output>
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59 </test>
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61 </tests>
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62 <help><![CDATA[
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64 **SnpSift Extract Fields**
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66 Extract fields from a VCF file to a TXT, tab separated format, that you can easily load in R, XLS, etc.
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68 http://snpeff.sourceforge.net/SnpSift.html#Extract
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70 You can also use sub-fields and genotype fields / sub-fields such as:
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71
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72 ::
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73
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74 Standard VCF fields:
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75 CHROM
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76 POS
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77 ID
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78 REF
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79 ALT
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80 FILTER
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81 INFO fields:
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82 AF
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83 AC
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84 DP
ed810da439cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12a2e9dd273b4c23db48bbb747f32700887710e
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85 MQ
14
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86 etc. (any info field available)
13
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87 SnpEff 'ANN' fields:
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88 "ANN[*].ALLELE" (alias GENOTYPE)
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89 "ANN[*].EFFECT" (alias ANNOTATION): Effect in Sequence ontology terms (e.g. 'missense_variant', 'synonymous_variant', 'stop_gained', etc.)
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90 "ANN[*].IMPACT" { HIGH, MODERATE, LOW, MODIFIER }
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91 "ANN[*].GENE" Gene name (e.g. 'PSD3')
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92 "ANN[*].GENEID" Gene ID
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93 "ANN[*].FEATURE"
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94 "ANN[*].FEATUREID" (alias TRID: Transcript ID)
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95 "ANN[*].BIOTYPE" Biotype, as described by the annotations (e.g. 'protein_coding')
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96 "ANN[*].RANK" Exon or Intron rank (i.e. exon number in a transcript)
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97 "ANN[*].HGVS_C" (alias HGVS_DNA, CODON): Variant in HGVS (DNA) notation
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98 "ANN[*].HGVS_P" (alias HGVS, HGVS_PROT, AA): Variant in HGVS (protein) notation
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99 "ANN[*].CDNA_POS" (alias POS_CDNA)
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100 "ANN[*].CDNA_LEN" (alias LEN_CDNA)
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101 "ANN[*].CDS_POS" (alias POS_CDS)
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102 "ANN[*].CDS_LEN" (alias LEN_CDS)
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103 "ANN[*].AA_POS" (alias POS_AA)
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104 "ANN[*].AA_LEN" (alias LEN_AA)
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105 "ANN[*].DISTANCE"
14
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106 "ANN[*].ERRORS" (alias WARNING, INFOS)
13
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107 SnpEff 'EFF' fields (this is for older SnpEff/SnpSift versions, new version use 'ANN' field):
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108 "EFF[*].EFFECT"
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109 "EFF[*].IMPACT"
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110 "EFF[*].FUNCLASS"
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111 "EFF[*].CODON"
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112 "EFF[*].AA"
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113 "EFF[*].AA_LEN"
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114 "EFF[*].GENE"
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115 "EFF[*].BIOTYPE"
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116 "EFF[*].CODING"
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117 "EFF[*].TRID"
14
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118 "EFF[*].RANK"
13
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119 SnpEff 'LOF' fields:
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120 "LOF[*].GENE"
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121 "LOF[*].GENEID"
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122 "LOF[*].NUMTR"
14
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123 "LOF[*].PERC"
13
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124 SnpEff' NMD' fields:
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125 "NMD[*].GENE"
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126 "NMD[*].GENEID"
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127 "NMD[*].NUMTR"
14
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128 "NMD[*].PERC"
13
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129
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130
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131 Some examples:
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132
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133 - *Extracting chromosome, position, ID and allele frequency from a VCF file:*
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134
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135 **CHROM POS ID AF**
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136
14
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137 The result will look something like:
13
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138
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139 ::
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140
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141 #CHROM POS ID AF
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142 1 69134 0.086
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143 1 69496 rs150690004 0.001
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144
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145
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146 - *Extracting genotype fields:*
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147
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148 **CHROM POS ID THETA GEN[0].GL[1] GEN[1].GL GEN[3].GL[*] GEN[*].GT**
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149
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150 This means to extract:
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151
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152 - CHROM POS ID: regular fields (as in the previous example)
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153 - THETA : This one is from INFO
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154 - GEN[0].GL[1] : Second likelihood from first genotype
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155 - GEN[1].GL : The whole GL fiels (all entries without separating them)
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156 - GEN[3].GL[*] : All likelihoods form genotype 3 (this time they will be tab separated, as opposed to the previous one).
14
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157 - GEN[*].GT : Genotype subfields (GT) from ALL samples (tab separated).
13
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158
14
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159 The result will look something like:
13
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160
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161 ::
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162
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163 #CHROM POS ID THETA GEN[0].GL[1] GEN[1].GL GEN[3].GL[*] GEN[*].GT
14
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164 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
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165 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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166 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
13
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167
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168 - *Extracting fields with multiple values:*
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169 (notice that there are multiple effect columns per line because there are mutiple effects per variant)
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170
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171 **CHROM POS REF ALT ANN[*].EFFECT**
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172
14
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173 The result will look something like:
13
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174
14
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175 ::
13
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176
ed810da439cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12a2e9dd273b4c23db48bbb747f32700887710e
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177 #CHROM POS REF ALT ANN[*].EFFECT
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178 22 17071756 T C 3_prime_UTR_variant downstream_gene_variant
ed810da439cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12a2e9dd273b4c23db48bbb747f32700887710e
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179 22 17072035 C T missense_variant downstream_gene_variant
ed810da439cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12a2e9dd273b4c23db48bbb747f32700887710e
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180 22 17072258 C A missense_variant downstream_gene_variant
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181
ed810da439cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12a2e9dd273b4c23db48bbb747f32700887710e
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182 - *Extracting fields with multiple values using a comma as a multipe field separator:*
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183
ed810da439cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12a2e9dd273b4c23db48bbb747f32700887710e
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184 **CHROM POS REF ALT ANN[*].EFFECT ANN[*].HGVS_P**
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185
14
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186 The result will look something like:
13
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187
14
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188 ::
13
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189
ed810da439cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12a2e9dd273b4c23db48bbb747f32700887710e
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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 .,.
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192 22 17072035 C T missense_variant,downstream_gene_variant p.Gly469Glu,.
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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
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196 - *Extracting fields with multiple values, one effect per line:*
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197
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198 **CHROM POS REF ALT ANN[*].EFFECT**
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199
14
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200 The result will look something like:
13
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201
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202 ::
13
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203
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204 #CHROM POS REF ALT ANN[*].EFFECT
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205 22 17071756 T C 3_prime_UTR_variant
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206 22 17071756 T C downstream_gene_variant
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207 22 17072035 C T missense_variant
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208 22 17072035 C T downstream_gene_variant
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209 22 17072258 C A missense_variant
ed810da439cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12a2e9dd273b4c23db48bbb747f32700887710e
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210 22 17072258 C A downstream_gene_variant
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211
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212
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213 @EXTERNAL_DOCUMENTATION@
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214 http://snpeff.sourceforge.net/SnpSift.html#Extract
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215
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216 ]]>
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217 </help>
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218 <expand macro="citations" />
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219 </tool>