<tool id="snp_filters" name="SNP filtering and pre-annotation">
  <requirements>
    <requirement type="package">SNVMix</requirement>
  </requirements>
  <description>further filtering and annotation of SNVMix calls</description>
  <command interpreter="python">
    snp_filters.py
      -i $input1
      -o $output1
      -c $output2
      -C $codon_resource
      -K $known_snp_resource
  </command>
 <inputs>
        <param name="input1" type="data" format="tabular" label="Select the filtered SNVMix output"></param>
	<param name="codon_resource" type="data" format="tabular" label="Select the codon_lookup file"></param>
        <param name="known_snp_resource" type="data" format="tabular" label="Select the all_known_snps file"></param>
 </inputs>
  <outputs>
    <data format="tabular" name="output1" label="${tool.name}: non-SNP positions" />
    <data format="tabular" name="output2" label="${tool.name}: Codon-associated non-SNP positions" />
  </outputs>
  <help>

**What it does**

  </help>
</tool>