<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>