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comparison snpSift_annotate.xml @ 24:f22f28cd881e

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Update for snpEff v3.2
author Jim Johnson <jj@umn.edu>
date Tue, 07 May 2013 14:58:15 -0500
parents 50c1a8ff6c82
children
comparison
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23:50c1a8ff6c82 24:f22f28cd881e
1 <tool id="snpSift_annotate" name="SnpSift Annotate" version="3.1"> 1 <tool id="snpSift_annotate" name="SnpSift Annotate" version="3.2">
2 <description>Annotate SNPs from dbSnp</description> 2 <description>Annotate SNPs from dbSnp</description>
3 <!-- 3 <!--
4 You will need to change the path to wherever your installation is. 4 You will need to change the path to wherever your installation is.
5 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)
6 --> 6 -->
7 <requirements> 7 <requirements>
8 <requirement type="package" version="3.1">snpEff</requirement> 8 <requirement type="package" version="3.2">snpEff</requirement>
9 </requirements> 9 </requirements>
10 <command>java -Xmx6G -jar \$JAVA_JAR_PATH/SnpSift.jar annotate -q $dbSnp $input > $output </command> 10 <command>
11 java -Xmx6G -jar \$JAVA_JAR_PATH/SnpSift.jar $annotate_cmd
12 #if $annotate.id :
13 -id
14 #elif $annotate.info_ids.__str__.strip() != '' :
15 -info "$annotate.info_ids"
16 #end if
17 -q $dbSnp $input > $output
18 </command>
11 <inputs> 19 <inputs>
12 <param format="vcf" name="input" type="data" label="VCF input"/> 20 <param format="vcf" name="input" type="data" label="VCF input"/>
13 <param format="vcf" name="dbSnp" type="data" label="VCF File with ID field annotated (e.g. dnSNP.vcf)" help="The ID field for a variant in input will be assigned from a matching variant in this file."/> 21 <param format="vcf" name="dbSnp" type="data" label="VCF File with ID field annotated (e.g. dnSNP.vcf)"
22 help="The ID field for a variant in input will be assigned from a matching variant in this file."/>
23 <param name="annotate_cmd" type="boolean" truevalue="annMem" falsevalue="annotate" checked="false" label="Annotate in Memory"
24 help="allows unsorted VCF files, but it loads the entire 'database' VCF file into memory (which may not be practical for large 'database' VCF files)"/>
25 <conditional name="annotate">
26 <param name="id" type="boolean" truevalue="id" falsevalue="info" checked="True" label="Only annotate ID field (do not add INFO field)" help=""/>
27 <when value="id"/>
28 <when value="info">
29 <param name="info_ids" type="text" value="" optional="true" label="Limit INFO annotation to these INFO IDs"
30 help="list is a comma separated list of fields. When blank, all INFO fields are included">
31 <validator type="regex" message="IDs separted by commas">^(([a-zA-Z][a-zA-Z0-9_-]*)(,[a-zA-Z][a-zA-Z0-9_-]*)*)?$</validator>
32 </param>
33 </when>
34 </conditional>
14 </inputs> 35 </inputs>
15 <stdio> 36 <stdio>
16 <exit_code range=":-1" level="fatal" description="Error: Cannot open file" /> 37 <exit_code range=":-1" level="fatal" description="Error: Cannot open file" />
17 <exit_code range="1:" level="fatal" description="Error" /> 38 <exit_code range="1:" level="fatal" description="Error" />
18 </stdio> 39 </stdio>
19 40
20 <outputs> 41 <outputs>
21 <data format="vcf" name="output" /> 42 <data format="vcf" name="output" />
22 </outputs> 43 </outputs>
23 44 <tests>
45 <test>
46 <param name="input" ftype="vcf" value="annotate_1.vcf"/>
47 <param name="dbSnp" ftype="vcf" value="db_test_1.vcf"/>
48 <param name="annotate_cmd" value="False"/>
49 <param name="id" value="True"/>
50 <output name="output">
51 <assert_contents>
52 <has_text text="rs76166080" />
53 </assert_contents>
54 </output>
55 </test>
56 </tests>
24 <help> 57 <help>
25 58
26 This is typically used to annotate IDs from dbSnp. 59 This is typically used to annotate IDs from dbSnp.
27 60
28 For details about this tool, please go to http://snpeff.sourceforge.net/SnpSift.html#annotate 61 For details about this tool, please go to http://snpeff.sourceforge.net/SnpSift.html#annotate