Mercurial > repos > jjohnson > snpsift
annotate snpSift_extractFields.xml @ 9:88f4997ccb02 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 93465571cf180554c3548338a68fa0f1604985dc-dirty
| author | jjohnson |
|---|---|
| date | Mon, 11 Apr 2016 09:31:49 -0400 |
| parents | 2f40467536cf |
| children |
| rev | line source |
|---|---|
| 4 | 1 <tool id="snpSift_extractFields" name="SnpSift Extract Fields" version="@WRAPPER_VERSION@.0"> |
| 2 <options sanitize="False" /> | |
| 3 <description>from a VCF file inot a tabular file</description> | |
| 4 <macros> | |
| 5 <import>snpSift_macros.xml</import> | |
| 6 </macros> | |
| 7 <expand macro="requirements" /> | |
| 8 <expand macro="stdio" /> | |
| 9 <expand macro="version_command" /> | |
| 10 <command><![CDATA[ | |
| 11 cat "$input" | |
| 12 #if $one_effect_per_line: | |
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2f40467536cf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 93465571cf180554c3548338a68fa0f1604985dc-dirty
jjohnson
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changeset
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13 | "\$SNPEFF_JAR_PATH/scripts/vcfEffOnePerLine.pl" |
| 4 | 14 #end if |
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2f40467536cf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 93465571cf180554c3548338a68fa0f1604985dc-dirty
jjohnson
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6
diff
changeset
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15 | java -Xmx6G -jar "\$SNPEFF_JAR_PATH/SnpSift.jar" extractFields |
| 4 | 16 #if $separator: |
| 17 -s '$separator' | |
| 18 #end if | |
| 19 #if $empty_text: | |
| 20 -e '$empty_text' | |
| 21 #end if | |
| 22 - | |
| 23 #echo ' '.join(['"%s"' % x for x in $extract.split()]) | |
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2f40467536cf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 93465571cf180554c3548338a68fa0f1604985dc-dirty
jjohnson
parents:
6
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changeset
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24 > "$output" |
| 4 | 25 ]]> |
| 26 </command> | |
| 27 <inputs> | |
| 28 <param format="vcf" name="input" type="data" label="Variant input file in VCF format"/> | |
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824f78c0d0df
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 915e0f28e6bc2701ca8f333d7b30cf399cd6e9da-dirty
jjohnson
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29 <param name="extract" type="text" label="Extract" help="Need help? See below a few examples." /> |
| 4 | 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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824f78c0d0df
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 915e0f28e6bc2701ca8f333d7b30cf399cd6e9da-dirty
jjohnson
parents:
4
diff
changeset
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31 <param name="separator" type="text" value="" optional="true" 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"> |
| 4 | 32 </param> |
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824f78c0d0df
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 915e0f28e6bc2701ca8f333d7b30cf399cd6e9da-dirty
jjohnson
parents:
4
diff
changeset
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33 <param name="empty_text" type="text" value="" optional="true" label="empty field text" help="Represent empty fields with this value, rather than leaving them blank" > |
| 4 | 34 </param> |
| 35 </inputs> | |
| 36 <outputs> | |
| 37 <data format="tabular" name="output" /> | |
| 38 </outputs> | |
| 39 <tests> | |
| 40 <test> | |
| 41 <param name="input" ftype="vcf" value="test_rmInfo.vcf"/> | |
| 42 <param name="extract" value="CHROM POS REF ALT EFF[*].EFFECT"/> | |
| 43 <output name="output"> | |
| 44 <assert_contents> | |
| 45 <has_text text="INTRAGENIC" /> | |
| 46 <not_has_text text="DOWNSTREAM,INTRAGENIC,INTRON,UTR_3_PRIME" /> | |
| 47 </assert_contents> | |
| 48 </output> | |
| 49 </test> | |
| 50 | |
| 51 <test> | |
| 52 <param name="input" ftype="vcf" value="test_rmInfo.vcf"/> | |
| 53 <param name="extract" value="CHROM POS REF ALT EFF[*].EFFECT"/> | |
| 54 <param name="separator" value=","/> | |
| 55 <output name="output"> | |
| 56 <assert_contents> | |
| 57 <has_text text="DOWNSTREAM,INTRAGENIC,INTRON,UTR_3_PRIME" /> | |
| 58 </assert_contents> | |
| 59 </output> | |
| 60 </test> | |
| 61 | |
| 62 </tests> | |
| 63 <help><![CDATA[ | |
| 64 | |
| 65 **SnpSift Extract Fields** | |
| 66 | |
| 67 Extract fields from a VCF file to a TXT, tab separated format, that you can easily load in R, XLS, etc. | |
| 68 | |
| 69 http://snpeff.sourceforge.net/SnpSift.html#Extract | |
| 70 | |
| 71 You can also use sub-fields and genotype fields / sub-fields such as: | |
| 72 | |
| 73 :: | |
| 74 | |
| 75 Standard VCF fields: | |
| 76 CHROM | |
| 77 POS | |
| 78 ID | |
| 79 REF | |
| 80 ALT | |
| 81 FILTER | |
| 82 INFO fields: | |
| 83 AF | |
| 84 AC | |
| 85 DP | |
| 86 MQ | |
| 87 etc. (any info field available) | |
| 88 SnpEff 'ANN' fields: | |
| 89 "ANN[*].ALLELE" (alias GENOTYPE) | |
| 90 "ANN[*].EFFECT" (alias ANNOTATION): Effect in Sequence ontology terms (e.g. 'missense_variant', 'synonymous_variant', 'stop_gained', etc.) | |
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824f78c0d0df
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 915e0f28e6bc2701ca8f333d7b30cf399cd6e9da-dirty
jjohnson
parents:
4
diff
changeset
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91 "ANN[*].IMPACT" { HIGH, MODERATE, LOW, MODIFIER } |
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824f78c0d0df
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 915e0f28e6bc2701ca8f333d7b30cf399cd6e9da-dirty
jjohnson
parents:
4
diff
changeset
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92 "ANN[*].GENE" Gene name (e.g. 'PSD3') |
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824f78c0d0df
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 915e0f28e6bc2701ca8f333d7b30cf399cd6e9da-dirty
jjohnson
parents:
4
diff
changeset
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93 "ANN[*].GENEID" Gene ID |
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824f78c0d0df
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 915e0f28e6bc2701ca8f333d7b30cf399cd6e9da-dirty
jjohnson
parents:
4
diff
changeset
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94 "ANN[*].FEATURE" |
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824f78c0d0df
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 915e0f28e6bc2701ca8f333d7b30cf399cd6e9da-dirty
jjohnson
parents:
4
diff
changeset
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95 "ANN[*].FEATUREID" (alias TRID: Transcript ID) |
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824f78c0d0df
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 915e0f28e6bc2701ca8f333d7b30cf399cd6e9da-dirty
jjohnson
parents:
4
diff
changeset
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96 "ANN[*].BIOTYPE" Biotype, as described by the annotations (e.g. 'protein_coding') |
|
824f78c0d0df
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 915e0f28e6bc2701ca8f333d7b30cf399cd6e9da-dirty
jjohnson
parents:
4
diff
changeset
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97 "ANN[*].RANK" Exon or Intron rank (i.e. exon number in a transcript) |
| 4 | 98 "ANN[*].HGVS_C" (alias HGVS_DNA, CODON): Variant in HGVS (DNA) notation |
| 99 "ANN[*].HGVS_P" (alias HGVS, HGVS_PROT, AA): Variant in HGVS (protein) notation | |
| 100 "ANN[*].CDNA_POS" (alias POS_CDNA) | |
| 101 "ANN[*].CDNA_LEN" (alias LEN_CDNA) | |
| 102 "ANN[*].CDS_POS" (alias POS_CDS) | |
| 103 "ANN[*].CDS_LEN" (alias LEN_CDS) | |
| 104 "ANN[*].AA_POS" (alias POS_AA) | |
| 105 "ANN[*].AA_LEN" (alias LEN_AA) | |
| 106 "ANN[*].DISTANCE" | |
| 107 "ANN[*].ERRORS" (alias WARNING, INFOS) | |
| 108 SnpEff 'EFF' fields (this is for older SnpEff/SnpSift versions, new version use 'ANN' field): | |
| 109 "EFF[*].EFFECT" | |
| 110 "EFF[*].IMPACT" | |
| 111 "EFF[*].FUNCLASS" | |
| 112 "EFF[*].CODON" | |
| 113 "EFF[*].AA" | |
| 114 "EFF[*].AA_LEN" | |
| 115 "EFF[*].GENE" | |
| 116 "EFF[*].BIOTYPE" | |
| 117 "EFF[*].CODING" | |
| 118 "EFF[*].TRID" | |
| 119 "EFF[*].RANK" | |
| 120 SnpEff 'LOF' fields: | |
| 121 "LOF[*].GENE" | |
| 122 "LOF[*].GENEID" | |
| 123 "LOF[*].NUMTR" | |
| 124 "LOF[*].PERC" | |
| 125 SnpEff' NMD' fields: | |
| 126 "NMD[*].GENE" | |
| 127 "NMD[*].GENEID" | |
| 128 "NMD[*].NUMTR" | |
| 129 "NMD[*].PERC" | |
| 130 | |
| 131 | |
| 132 Some examples: | |
| 133 | |
| 134 - *Extracting chromosome, position, ID and allele frequency from a VCF file:* | |
| 135 | |
| 136 **CHROM POS ID AF** | |
| 137 | |
| 138 The result will look something like: | |
| 139 | |
| 140 :: | |
| 141 | |
| 142 #CHROM POS ID AF | |
| 143 1 69134 0.086 | |
| 144 1 69496 rs150690004 0.001 | |
| 145 | |
| 146 | |
| 147 - *Extracting genotype fields:* | |
| 148 | |
| 149 **CHROM POS ID THETA GEN[0].GL[1] GEN[1].GL GEN[3].GL[*] GEN[*].GT** | |
| 150 | |
| 151 This means to extract: | |
| 152 | |
| 153 - CHROM POS ID: regular fields (as in the previous example) | |
| 154 - THETA : This one is from INFO | |
| 155 - GEN[0].GL[1] : Second likelihood from first genotype | |
| 156 - GEN[1].GL : The whole GL fiels (all entries without separating them) | |
| 157 - GEN[3].GL[*] : All likelihoods form genotype 3 (this time they will be tab separated, as opposed to the previous one). | |
| 158 - GEN[*].GT : Genotype subfields (GT) from ALL samples (tab separated). | |
| 159 | |
| 160 The result will look something like: | |
| 161 | |
| 162 :: | |
| 163 | |
| 164 #CHROM POS ID THETA GEN[0].GL[1] GEN[1].GL GEN[3].GL[*] GEN[*].GT | |
| 165 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 | |
| 166 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 | |
| 167 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 | |
| 168 | |
| 169 - *Extracting fields with multiple values:* | |
| 170 (notice that there are multiple effect columns per line because there are mutiple effects per variant) | |
| 171 | |
| 172 **CHROM POS REF ALT ANN[*].EFFECT** | |
| 173 | |
| 174 The result will look something like: | |
| 175 | |
| 176 :: | |
| 177 | |
| 178 #CHROM POS REF ALT ANN[*].EFFECT | |
| 179 22 17071756 T C 3_prime_UTR_variant downstream_gene_variant | |
| 180 22 17072035 C T missense_variant downstream_gene_variant | |
| 181 22 17072258 C A missense_variant downstream_gene_variant | |
| 182 | |
| 183 - *Extracting fields with multiple values using a comma as a multipe field separator:* | |
| 184 | |
| 185 **CHROM POS REF ALT ANN[*].EFFECT ANN[*].HGVS_P** | |
| 186 | |
| 187 The result will look something like: | |
| 188 | |
| 189 :: | |
| 190 | |
| 191 #CHROM POS REF ALT ANN[*].EFFECT ANN[*].HGVS_P | |
| 192 22 17071756 T C 3_prime_UTR_variant,downstream_gene_variant .,. | |
| 193 22 17072035 C T missense_variant,downstream_gene_variant p.Gly469Glu,. | |
| 194 22 17072258 C A missense_variant,downstream_gene_variant p.Gly395Cys,. | |
| 195 | |
| 196 | |
| 197 - *Extracting fields with multiple values, one effect per line:* | |
| 198 | |
| 199 **CHROM POS REF ALT ANN[*].EFFECT** | |
| 200 | |
| 201 The result will look something like: | |
| 202 | |
| 203 :: | |
| 204 | |
| 205 #CHROM POS REF ALT ANN[*].EFFECT | |
| 206 22 17071756 T C 3_prime_UTR_variant | |
| 207 22 17071756 T C downstream_gene_variant | |
| 208 22 17072035 C T missense_variant | |
| 209 22 17072035 C T downstream_gene_variant | |
| 210 22 17072258 C A missense_variant | |
| 211 22 17072258 C A downstream_gene_variant | |
| 212 | |
| 213 | |
| 214 @EXTERNAL_DOCUMENTATION@ | |
| 215 http://snpeff.sourceforge.net/SnpSift.html#Extract | |
| 216 | |
| 217 ]]> | |
| 218 </help> | |
|
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2f40467536cf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 93465571cf180554c3548338a68fa0f1604985dc-dirty
jjohnson
parents:
6
diff
changeset
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219 <expand macro="citations" /> |
| 4 | 220 </tool> |