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1 <tool id="snpSift_int" name="SnpSift Intervals" version="1.0">
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2 <description>Filter variants using intervals </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>
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12 cat $input | java -Xmx2G -jar $JAVA_JAR_PATH/SnpSift.jar int $bedFile > $output
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13 </command>
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14 <inputs>
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15 <param format="vcf" name="input" type="data" label="VCF input"/>
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16 <param format="bed" name="bedFile" type="data" label="Intervals (BED file)"/>
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17 </inputs>
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18 <outputs>
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19 <data format="vcf" name="output" />
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20 </outputs>
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5
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21 <stdio>
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22 <exit_code range=":-1" level="fatal" description="Error: Cannot open file" />
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23 <exit_code range="1:" level="fatal" description="Error" />
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24 </stdio>
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25 <help>
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26
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27 You can filter using intervals (BED file)
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28
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29 For details about this tool, please go to http://snpeff.sourceforge.net/SnpSift.html#intervals
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30
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31 </help>
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32 </tool>
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