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1 <tool id="varscan" name="VarScan Readcount" version="1">
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2 <description>To use varscan readcount tool</description>
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3 <requirements>
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4 <requirement type="package" version="2.4.4">varscan</requirement>
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5 </requirements>
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6 <command detect_errors="exit_code"><![CDATA[
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7 varscan readcounts ${input} --min-coverage ${min_cov} --min-base-qual ${min_base_qual} --output-file ${output}
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8 ]]></command>
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9 <inputs>
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10 <param format="pileup" name="input" type="data" label="Pileup dataset" help=""/>
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11 <param name="min_cov" type="integer" value="1" min="1" max="2000" label="Minimum read depth" help="Minimum depth at a position to make a call [1]"/>
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12 <param name="min_base_qual" type="integer" value="20" min="1" max="500" label="Minimum base quality" label="Minimum base quality at a position to count a read [20]"/>
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13 </inputs>
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14 <outputs>
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15 <data name="output" format="vcf"/>
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16 </outputs>
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17 <help>
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18 command: varscan readcounts --help
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19
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20 Min coverage: 1
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21 Min base qual: 20
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22 USAGE: java -jar VarScan.jar readcounts pileup_file OPTIONS
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23 OPTIONS:
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24 --variants-file A list of variants at which to report readcounts
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25 --output-file Output file to contain the readcounts
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26 --min-coverage Minimum read depth at a position to make a call (1)
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27 --min-base-qual Minimum base quality at a position to count a read (20)
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28 </help>
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29 </tool>
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