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comparison snpSift_annotate.xml @ 8:13b6ad2ddace

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SnpEffect v3.2
author Jim Johnson <jj@umn.edu>
date Mon, 13 May 2013 12:45:07 -0500
parents 192a236898f5
children 937367efb1da
comparison
equal deleted inserted replaced
7:b26a1aff7f81 8:13b6ad2ddace
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>
22 </outputs> 43 </outputs>
23 <tests> 44 <tests>
24 <test> 45 <test>
25 <param name="input" ftype="vcf" value="annotate_1.vcf"/> 46 <param name="input" ftype="vcf" value="annotate_1.vcf"/>
26 <param name="dbSnp" ftype="vcf" value="db_test_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"/>
27 <output name="output"> 50 <output name="output">
28 <assert_contents> 51 <assert_contents>
29 <has_text text="rs76166080" /> 52 <has_text text="rs76166080" />
30 </assert_contents> 53 </assert_contents>
31 </output> 54 </output>