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1 <tool id="snpSift_annotate" name="SnpSift Annotate" version="3.1">
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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="3.1">snpEff</requirement>
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9 </requirements>
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10 <command>java -Xmx6G -jar \$JAVA_JAR_PATH/SnpSift.jar annotate -q $dbSnp $input > $output </command>
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11 <inputs>
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12 <param format="vcf" name="input" type="data" label="VCF input"/>
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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."/>
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14 </inputs>
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15 <stdio>
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16 <exit_code range=":-1" level="fatal" description="Error: Cannot open file" />
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17 <exit_code range="1:" level="fatal" description="Error" />
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18 </stdio>
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19
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20 <outputs>
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21 <data format="vcf" name="output" />
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22 </outputs>
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5
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23 <tests>
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24 <test>
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25 <param name="input" ftype="vcf" value="annotate_1.vcf"/>
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26 <param name="dbSnp" ftype="vcf" value="db_test_1.vcf"/>
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27 <output name="output">
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28 <assert_contents>
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29 <has_text text="rs76166080" />
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30 </assert_contents>
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31 </output>
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32 </test>
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33 </tests>
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34 <help>
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35
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36 This is typically used to annotate IDs from dbSnp.
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37
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38 For details about this tool, please go to http://snpeff.sourceforge.net/SnpSift.html#annotate
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39
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40 </help>
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41 </tool>
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42
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