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comparison snpSift_annotate.xml @ 7:0ad9733e22a4

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author bgruening
date Fri, 29 Nov 2013 09:27:22 -0500
parents 8952990fcab9
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6:eb394dd65c98 7:0ad9733e22a4
1 <tool id="snpSift_annotate" name="SnpSift Annotate" version="3.4"> 1 <tool id="snpSift_annotate" name="SnpSift Annotate" version="3.4">
2 <description>Annotate SNPs from dbSnp</description> 2 <description>SNPs from dbSnp</description>
3 <!-- 3 <!--
4 You will need to change the path to wherever your installation is. 4 You can change the amount of memory used, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory)
5 You can change the amount of memory used, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory) 5 -->
6 --> 6 <expand macro="requirements" />
7 <requirements> 7 <macros>
8 <requirement type="package" version="3.4">snpEff</requirement> 8 <import>snpEff_macros.xml</import>
9 </requirements> 9 </macros>
10 <command> 10 <command>
11 java -Xmx6G -jar \$SNPEFF_JAR_PATH/SnpSift.jar $annotate_cmd 11 java -Xmx6G -jar \$SNPEFF_JAR_PATH/SnpSift.jar $annotate_cmd
12 #if $annotate.id : 12 #if $annotate.id :
13 -id 13 -id
14 #elif $annotate.info_ids.__str__.strip() != '' : 14 #elif $annotate.info_ids.__str__.strip() != '' :
15 -info "$annotate.info_ids" 15 -info "$annotate.info_ids"
16 #end if 16 #end if
17 -q $dbSnp $input > $output 17 -q $dbSnp $input > $output
18 </command> 18 </command>
19 <inputs> 19 <inputs>
20 <param format="vcf" name="input" type="data" label="VCF input"/> 20 <param format="vcf" name="input" type="data" label="Variant input file in VCF format"/>
21 <param format="vcf" name="dbSnp" type="data" label="VCF File with ID field annotated (e.g. dnSNP.vcf)" 21 <param format="vcf" name="dbSnp" type="data" label="VCF File with ID field annotated (e.g. dnSNP.vcf)"
22 help="The ID field for a variant in input will be assigned from a matching variant in this file."/> 22 help="The ID field for a variant in input will be assigned from a matching variant in this file."/>
23 <conditional name="annotate"> 23 <conditional name="annotate">
24 <param name="id" type="boolean" truevalue="id" falsevalue="info" checked="True" label="Only annotate ID field (do not add INFO field)" help=""/> 24 <param name="id" type="boolean" truevalue="id" falsevalue="info" checked="True" label="Only annotate ID field (do not add INFO field)" help=""/>
25 <when value="id"/> 25 <when value="id"/>
26 <when value="info"> 26 <when value="info">
27 <param name="info_ids" type="text" value="" size="60" optional="true" label="Limit INFO annotation to these INFO IDs" 27 <param name="info_ids" type="text" value="" size="60" optional="true" label="Limit INFO annotation to these INFO IDs"
28 help="list is a comma separated list of fields. When blank, all INFO fields are included"> 28 help="list is a comma separated list of fields. When blank, all INFO fields are included">
29 <validator type="regex" message="IDs separted by commas">^(([a-zA-Z][a-zA-Z0-9_-]*)(,[a-zA-Z][a-zA-Z0-9_-]*)*)?$</validator> 29 <validator type="regex" message="IDs separted by commas">^(([a-zA-Z][a-zA-Z0-9_-]*)(,[a-zA-Z][a-zA-Z0-9_-]*)*)?$</validator>
30 </param>
31 </when>
32 </conditional>
33 <param name="annotate_cmd" type="boolean" truevalue="annMem" falsevalue="annotate" checked="false" label="Annotate in Memory">
34 <help>
35 Allows unsorted VCF files, but it loads the entire 'database' VCF file into memory (which may not be practical for large 'database' VCF files).
36 Otherwise, both the database and the input VCF files should be sorted by position (Chromosome sort order can differ between files).
37 </help>
38 </param> 30 </param>
39 </inputs> 31 </when>
40 <stdio> 32 </conditional>
41 <exit_code range=":-1" level="fatal" description="Error: Cannot open file" /> 33 <param name="annotate_cmd" type="boolean" truevalue="annMem" falsevalue="annotate" checked="false" label="Allow unsorted VCF files">
42 <exit_code range="1:" level="fatal" description="Error" /> 34 <help>
43 </stdio> 35 This option will load the entire 'database' VCF file into memory (which may not be practical for large 'database' VCF files).
44 36 Otherwise, both the database and the input VCF files should be sorted by position (Chromosome sort order can differ between files).
45 <outputs> 37 </help>
46 <data format="vcf" name="output" /> 38 </param>
47 </outputs> 39 </inputs>
48 <tests> 40 <expand macro="stdio" />
49 <test> 41 <outputs>
50 <param name="input" ftype="vcf" value="annotate_1.vcf"/> 42 <data format="vcf" name="output" />
51 <param name="dbSnp" ftype="vcf" value="db_test_1.vcf"/> 43 </outputs>
52 <param name="annotate_cmd" value="False"/> 44 <tests>
53 <param name="id" value="True"/> 45 <test>
54 <output name="output"> 46 <param name="input" ftype="vcf" value="annotate_1.vcf"/>
55 <assert_contents> 47 <param name="dbSnp" ftype="vcf" value="db_test_1.vcf"/>
56 <has_text text="rs76166080" /> 48 <param name="annotate_cmd" value="False"/>
57 </assert_contents> 49 <param name="id" value="True"/>
58 </output> 50 <output name="output">
59 </test> 51 <assert_contents>
60 </tests> 52 <has_text text="rs76166080" />
61 <help> 53 </assert_contents>
54 </output>
55 </test>
56 </tests>
57 <help>
62 58
63 This is typically used to annotate IDs from dbSnp. 59 This is typically used to annotate IDs from dbSnp.
64
65 For details about this tool, please go to http://snpeff.sourceforge.net/SnpSift.html#annotate
66 60
67 Annotatating only the ID field from dbSnp137.vcf :: 61 Annotatating only the ID field from dbSnp137.vcf ::
68 62
69 Input VCF: 63 Input VCF:
70 CHROM POS ID REF ALT QUAL FILTER INFO 64 CHROM POS ID REF ALT QUAL FILTER INFO
93 22 16157571 . T G 0.0 FAIL NS=53 87 22 16157571 . T G 0.0 FAIL NS=53
94 22 16346045 rs56234788 T C 0.0 FAIL NS=244;RSPOS=16346045;GMAF=0.162248628884826;dbSNPBuildID=129;SSR=0;SAO=0;VP=050100000000000100000100;WGT=0;VC=SNV;SLO;GNO 88 22 16346045 rs56234788 T C 0.0 FAIL NS=244;RSPOS=16346045;GMAF=0.162248628884826;dbSNPBuildID=129;SSR=0;SAO=0;VP=050100000000000100000100;WGT=0;VC=SNV;SLO;GNO
95 22 16350245 rs2905295 C A 0.0 FAIL NS=192;RSPOS=16350245;GMAF=0.230804387568556;dbSNPBuildID=101;SSR=1;SAO=0;VP=050000000000000100000140;WGT=0;VC=SNV;GNO 89 22 16350245 rs2905295 C A 0.0 FAIL NS=192;RSPOS=16350245;GMAF=0.230804387568556;dbSNPBuildID=101;SSR=1;SAO=0;VP=050000000000000100000140;WGT=0;VC=SNV;GNO
96 90
97 91
98 SnpEff citation: 92 @EXTERNAL_DOCUMENTATION@
99 "A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3.", Cingolani P, Platts A, Wang le L, Coon M, Nguyen T, Wang L, Land SJ, Lu X, Ruden DM. Fly (Austin). 2012 Apr-Jun;6(2):80-92. PMID: 22728672 [PubMed - in process]
100 93
101 SnpSift citation: 94 @CITATION_SECTION@
102 "Using Drosophila melanogaster as a model for genotoxic chemical mutational studies with a new program, SnpSift", Cingolani, P., et. al., Frontiers in Genetics, 3, 2012.
103 95
104 96
105 </help> 97 </help>
106 </tool> 98 </tool>
107 99