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

  <command interpreter="python">
    nucleotide_diversity_pi.py "$saps" "$snps" "$intervals" "$indivs" "$output"
    #for $individual_name, $individual_col in zip($snps.dataset.metadata.individual_names, $snps.dataset.metadata.individual_columns)
      #set $arg = '%s:%s' % ($individual_col, $individual_name)
      "$arg"
    #end for
  </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>

  <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>