Mercurial > repos > jjohnson > snpeff_with_dep

annotate snpSift_int.xml @ 0:388f178f9e13

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author jjohnson
date Thu, 13 Sep 2012 22:33:33 -0400
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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="set_environment">JAVA_JAR_PATH </requirement>
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9 </requirements>
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10 <command>
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11 cat $input | java -Xmx2G -jar $JAVA_JAR_PATH/SnpSift.jar int $bedFile > $output
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12 </command>
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13 <inputs>
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14 <param format="vcf" name="input" type="data" label="VCF input"/>
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15 <param format="bed" name="bedFile" type="data" label="Intervals (BED file)"/>
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16 </inputs>
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17 <outputs>
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18 <data format="vcf" name="output" />
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19 </outputs>
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20
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21 <help>
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22
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23 You can filter using intervals (BED file)
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24
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25 For details about this tool, please go to http://snpeff.sourceforge.net/SnpSift.html#intervals
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26
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27 </help>
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28 </tool>