<tool id="gd_nucleotide_diversity_pi" name="Nucleotide Diversity" version="1.0.0">
  <description>: &amp;pi; and &amp;theta;</description>

  <command interpreter="python">
    #import json
    #import base64
    #import zlib
    #set $ind_names = $snps.dataset.metadata.individual_names
    #set $ind_colms = $snps.dataset.metadata.individual_columns
    #set $ind_dict = dict(zip($ind_names, $ind_colms))
    #set $ind_json = json.dumps($ind_dict, separators=(',',':'))
    #set $ind_comp = zlib.compress($ind_json, 9)
    #set $ind_arg = base64.b64encode($ind_comp)
    nucleotide_diversity_pi.py '$saps' '$snps' '$intervals' '$indivs' '$output' '$ind_arg'
  </command>

  <inputs>
    <param name="saps" type="data" format="gd_sap" label="SAP Dataset" />
    <param name="snps" type="data" format="gd_snp" label="SNP Dataset" />
    <param name="intervals" type="data" format="gd_covered_cds" label="Covered intervals" />
    <param name="indivs" type="data" format="gd_indivs" label="Population individuals" />
  </inputs>

  <outputs>
    <data name="output" format="txt" />
  </outputs>

  <requirements>
    <requirement type="package" version="0.1">gd_c_tools</requirement>
  </requirements>

  <help>
**What it does**

This tool computes values that estimate some basic parameters.

**Output**

the number of nonsyn SNPs, total number of nonsynon sites, piNon,
the number of synon SNPs, total number of synon sites, piSyn, plus
total length of covered intervals, thetaNon, thetaSyn
  </help>
</tool>