Mercurial > repos > ryanmorin > nextgen_variant_identification
view SNV/filter_snvmix.xml @ 0:74f5ea818cea
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author | ryanmorin |
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date | Wed, 12 Oct 2011 19:50:38 -0400 |
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<tool id="filter_snvmix" name="SNVMix filter"> <requirements> <requirement type="package">SNVMix</requirement> </requirements> <description>post-filtration for SNVMix calls</description> <command interpreter="python"> filter_snvmix.py -s $input1 -o $output1 -S $require_dual_strand -i $max_indels </command> <inputs> <param name="input1" type="data" format="tabular" label="Select the raw SNVMix output to be filtered"></param> <param name="require_dual_strand" type="select" label="Require support from both strands? (recommended)"> <option selected="true" value="yes">Yes</option> <option value="no">No</option> </param> <param name="max_indels" type="integer" value="2" label="maximum number of indels in reads supporting variant"> </param> </inputs> <outputs> <data format="tabular" name="output1" label="${tool.name}: Filtered SNVMix calls" /> </outputs> <help> **What it does** This tool uses a set of thresholds on SNVMix p value and sequence context to reduce the list to likely true variants </help> </tool>