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1 <tool id="snpSift_annotate" name="SnpSift Annotate" version="1.0">
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2 <description>Annotate SNPs from dbSnp</description>
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3 <!--
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4 You will need to change the path to wherever your installation is.
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5 You can change the amount of memory used, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory)
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6 -->
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7 <requirements>
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8 <requirement type="package" version="3.0f">snpEff</requirement>
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9 <requirement type="set_environment">JAVA_JAR_PATH </requirement>
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10 </requirements>
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11 <command>java -Xmx6G -jar $JAVA_JAR_PATH/SnpSift.jar annotate -q $dbSnp $input > $output </command>
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12 <inputs>
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13 <param format="vcf" name="input" type="data" label="VCF input"/>
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14 <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."/>
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15 </inputs>
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16 <stdio>
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17 <exit_code range=":-1" level="fatal" description="Error: Cannot open file" />
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18 <exit_code range="1:" level="fatal" description="Error" />
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19 </stdio>
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20
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21 <outputs>
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22 <data format="vcf" name="output" />
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23 </outputs>
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24
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25 <help>
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26
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27 This is typically used to annotate IDs from dbSnp.
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28
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29 For details about this tool, please go to http://snpeff.sourceforge.net/SnpSift.html#annotate
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30
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31 </help>
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32 </tool>
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33
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