Mercurial > repos > iuc > snpsift

annotate snpSift_extractFields.xml @ 3:20c7d583fec1 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
author iuc
date Mon, 12 Jun 2017 10:25:32 -0400
parents bf8c1526871b
children 09d6806c609e
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
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iuc
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1 <tool id="snpSift_extractFields" name="SnpSift Extract Fields" version="@WRAPPER_VERSION@.0">
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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@ &&
20c7d583fec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
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12 cat '$input'
20c7d583fec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
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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 | SnpSift -Xmx6G extractFields
20c7d583fec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
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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 $empty_text:
20c7d583fec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
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21 -e '$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 $extract.split()])
20c7d583fec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
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25 > '$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="Extract" help="Need help? See below a few examples." />
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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" />
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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" />
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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
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49 <test>
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50 <param name="input" ftype="vcf" value="test_rmInfo.vcf"/>
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51 <param name="extract" value="CHROM POS REF ALT EFF[*].EFFECT"/>
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52 <param name="separator" value=","/>
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53 <output name="output">
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54 <assert_contents>
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55 <has_text text="DOWNSTREAM,INTRAGENIC,INTRON,UTR_3_PRIME" />
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56 </assert_contents>
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57 </output>
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58 </test>
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59 </tests>
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60 <help><![CDATA[
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61 **SnpSift Extract Fields**
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62
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63 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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64
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65 http://snpeff.sourceforge.net/SnpSift.html#Extract
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66
3
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67 You can also use sub-fields and genotype fields / sub-fields such as::
1
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68
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69 Standard VCF fields:
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70 CHROM
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71 POS
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72 ID
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73 REF
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74 ALT
2
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75 FILTER
1
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76 INFO fields:
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77 AF
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78 AC
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79 DP
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80 MQ
2
bf8c1526871b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f
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81 etc. (any info field available)
1
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82 SnpEff 'ANN' fields:
98708b88af9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
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83 "ANN[*].ALLELE" (alias GENOTYPE)
98708b88af9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
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84 "ANN[*].EFFECT" (alias ANNOTATION): Effect in Sequence ontology terms (e.g. 'missense_variant', 'synonymous_variant', 'stop_gained', etc.)
98708b88af9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
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85 "ANN[*].IMPACT" { HIGH, MODERATE, LOW, MODIFIER }
98708b88af9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
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86 "ANN[*].GENE" Gene name (e.g. 'PSD3')
98708b88af9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
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87 "ANN[*].GENEID" Gene ID
98708b88af9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
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88 "ANN[*].FEATURE"
98708b88af9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
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89 "ANN[*].FEATUREID" (alias TRID: Transcript ID)
98708b88af9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
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90 "ANN[*].BIOTYPE" Biotype, as described by the annotations (e.g. 'protein_coding')
98708b88af9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
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91 "ANN[*].RANK" Exon or Intron rank (i.e. exon number in a transcript)
98708b88af9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
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92 "ANN[*].HGVS_C" (alias HGVS_DNA, CODON): Variant in HGVS (DNA) notation
98708b88af9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
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93 "ANN[*].HGVS_P" (alias HGVS, HGVS_PROT, AA): Variant in HGVS (protein) notation
98708b88af9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
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94 "ANN[*].CDNA_POS" (alias POS_CDNA)
98708b88af9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
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95 "ANN[*].CDNA_LEN" (alias LEN_CDNA)
98708b88af9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
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96 "ANN[*].CDS_POS" (alias POS_CDS)
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97 "ANN[*].CDS_LEN" (alias LEN_CDS)
98708b88af9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
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98 "ANN[*].AA_POS" (alias POS_AA)
98708b88af9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
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99 "ANN[*].AA_LEN" (alias LEN_AA)
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100 "ANN[*].DISTANCE"
2
bf8c1526871b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f
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101 "ANN[*].ERRORS" (alias WARNING, INFOS)
1
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102 SnpEff 'EFF' fields (this is for older SnpEff/SnpSift versions, new version use 'ANN' field):
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103 "EFF[*].EFFECT"
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104 "EFF[*].IMPACT"
98708b88af9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
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105 "EFF[*].FUNCLASS"
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106 "EFF[*].CODON"
98708b88af9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
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107 "EFF[*].AA"
98708b88af9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
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108 "EFF[*].AA_LEN"
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109 "EFF[*].GENE"
98708b88af9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
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110 "EFF[*].BIOTYPE"
98708b88af9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
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111 "EFF[*].CODING"
98708b88af9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
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112 "EFF[*].TRID"
2
bf8c1526871b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f
iuc
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113 "EFF[*].RANK"
1
98708b88af9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
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114 SnpEff 'LOF' fields:
98708b88af9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
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115 "LOF[*].GENE"
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116 "LOF[*].GENEID"
98708b88af9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
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117 "LOF[*].NUMTR"
2
bf8c1526871b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f
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118 "LOF[*].PERC"
1
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119 SnpEff' NMD' fields:
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120 "NMD[*].GENE"
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121 "NMD[*].GENEID"
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122 "NMD[*].NUMTR"
2
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123 "NMD[*].PERC"
1
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124
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125 Some examples:
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126
3
20c7d583fec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
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127 - *Extracting chromosome, position, ID and allele frequency from a VCF file*:
1
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128
3
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129 **CHROM POS ID AF**
1
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130
3
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131 The result will look something like::
1
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132
3
20c7d583fec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
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133 #CHROM POS ID AF
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iuc
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134 1 69134 0.086
20c7d583fec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
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135 1 69496 rs150690004 0.001
1
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136
3
20c7d583fec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
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137 - *Extracting genotype fields*:
1
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138
3
20c7d583fec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
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139 **CHROM POS ID THETA GEN[0].GL[1] GEN[1].GL GEN[3].GL[*] GEN[*].GT**
1
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140
3
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141 This means to extract:
1
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142
3
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143 - CHROM POS ID: regular fields (as in the previous example)
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144 - THETA : This one is from INFO
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145 - GEN[0].GL[1] : Second likelihood from first genotype
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146 - GEN[1].GL : The whole GL fiels (all entries without separating them)
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147 - GEN[3].GL[*] : All likelihoods form genotype 3 (this time they will be tab separated, as opposed to the previous one).
20c7d583fec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
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148 - GEN[*].GT : Genotype subfields (GT) from ALL samples (tab separated).
1
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149
3
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150 The result will look something like::
1
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151
3
20c7d583fec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
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152 #CHROM POS ID THETA GEN[0].GL[1] GEN[1].GL GEN[3].GL[*] GEN[*].GT
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153 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
20c7d583fec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
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154 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
20c7d583fec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
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155 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
1
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156
3
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157 - *Extracting fields with multiple values*:
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158 (notice that there are multiple effect columns per line because there are mutiple effects per variant)
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159
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160 **CHROM POS REF ALT ANN[*].EFFECT**
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161
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162 The result will look something like::
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163
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164 #CHROM POS REF ALT ANN[*].EFFECT
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165 22 17071756 T C 3_prime_UTR_variant downstream_gene_variant
20c7d583fec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
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166 22 17072035 C T missense_variant downstream_gene_variant
20c7d583fec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
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167 22 17072258 C A missense_variant downstream_gene_variant
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168
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169 - *Extracting fields with multiple values using a comma as a multipe field separator:*
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170
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171 **CHROM POS REF ALT ANN[*].EFFECT ANN[*].HGVS_P**
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172
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173 The result will look something like::
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174
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175 #CHROM POS REF ALT ANN[*].EFFECT ANN[*].HGVS_P
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176 22 17071756 T C 3_prime_UTR_variant,downstream_gene_variant .,.
20c7d583fec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
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177 22 17072035 C T missense_variant,downstream_gene_variant p.Gly469Glu,.
20c7d583fec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
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178 22 17072258 C A missense_variant,downstream_gene_variant p.Gly395Cys,.
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179
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180 - *Extracting fields with multiple values, one effect per line:*
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181
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182 **CHROM POS REF ALT ANN[*].EFFECT**
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183
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184 The result will look something like::
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185
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186 #CHROM POS REF ALT ANN[*].EFFECT
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187 22 17071756 T C 3_prime_UTR_variant
20c7d583fec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
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188 22 17071756 T C downstream_gene_variant
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189 22 17072035 C T missense_variant
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190 22 17072035 C T downstream_gene_variant
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191 22 17072258 C A missense_variant
20c7d583fec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
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192 22 17072258 C A downstream_gene_variant
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193
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194 @EXTERNAL_DOCUMENTATION@
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195 - http://snpeff.sourceforge.net/SnpSift.html#Extract
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196 ]]></help>
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197 <expand macro="citations" />
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198 </tool>