Mercurial > repos > greg > snpeff_v2_from_pablo

annotate snpEff_2_1a/galaxy/snpSift_int.xml @ 0:f8eaa3f8194b default tip

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Uploaded snpEff_v2_1a_core.tgz from Pablo Cingolani
author greg
date Fri, 20 Apr 2012 14:47:09 -0400
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f8eaa3f8194b Uploaded snpEff_v2_1a_core.tgz from Pablo Cingolani
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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 <command>
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8 cat $input | java -Xmx2G -jar /home/pcingola/tools/SnpSift.jar int $bedFile > $output
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9 </command>
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10 <inputs>
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11 <param format="Tabular" name="input" type="data" label="VCF input"/>
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12 <param format="Tabular" name="bedFile" type="data" label="Intervals (BED file)"/>
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13 </inputs>
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14 <outputs>
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15 <data format="tabular" name="output" />
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16 </outputs>
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17
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18 <help>
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19
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20 You can filter using intervals (BED file)
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21
f8eaa3f8194b Uploaded snpEff_v2_1a_core.tgz from Pablo Cingolani
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22 For details about this tool, please go to http://snpeff.sourceforge.net/SnpSift.html#intervals
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23
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24 </help>
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25 </tool>