|
0
|
1 <tool id="snpSift_annotate" name="SnpSift Annotate" version="1.0">
|
|
|
2 <description>Annotate SNPs from dbSnp</description>
|
|
|
3 <!--
|
|
|
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)
|
|
|
6 -->
|
|
|
7 <requirements>
|
|
|
8 <requirement type="package" version="1.7">SnpSift</requirement>
|
|
|
9 </requirements>
|
|
|
10 <command>java -Xmx6G -jar \$JAVA_JAR_PATH/SnpSift.jar annotate -q $dbSnp $input > $output </command>
|
|
|
11 <inputs>
|
|
|
12 <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."/>
|
|
|
14 </inputs>
|
|
|
15 <stdio>
|
|
|
16 <exit_code range=":-1" level="fatal" description="Error: Cannot open file" />
|
|
|
17 <exit_code range="1:" level="fatal" description="Error" />
|
|
|
18 </stdio>
|
|
|
19
|
|
|
20 <outputs>
|
|
|
21 <data format="vcf" name="output" />
|
|
|
22 </outputs>
|
|
|
23
|
|
|
24 <help>
|
|
|
25
|
|
|
26 This is typically used to annotate IDs from dbSnp.
|
|
|
27
|
|
|
28 For details about this tool, please go to http://snpeff.sourceforge.net/SnpSift.html#annotate
|
|
|
29
|
|
|
30 </help>
|
|
|
31 </tool>
|
|
|
32
|
