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1 <tool id="filter_snvmix" name="SNVMix filter">
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2 <requirements>
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3 <requirement type="package">SNVMix</requirement>
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4 </requirements>
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5 <description>post-filtration for SNVMix calls</description>
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6 <command interpreter="python">
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7 filter_snvmix.py
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8 -s $input1
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9 -o $output1
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10 -S $require_dual_strand
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11 -i $max_indels
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12 </command>
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13 <inputs>
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14 <param name="input1" type="data" format="tabular" label="Select the raw SNVMix output to be filtered"></param>
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15 <param name="require_dual_strand" type="select" label="Require support from both strands? (recommended)">
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16 <option selected="true" value="yes">Yes</option>
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17 <option value="no">No</option>
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18 </param>
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19 <param name="max_indels" type="integer" value="2" label="maximum number of indels in reads supporting variant">
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20 </param>
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21 </inputs>
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22 <outputs>
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23 <data format="tabular" name="output1" label="${tool.name}: Filtered SNVMix calls" />
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24 </outputs>
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25 <help>
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26
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27 **What it does**
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28
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29 This tool uses a set of thresholds on SNVMix p value and sequence context to reduce the list to likely true variants
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30
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31 </help>
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32 </tool>
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