<tool id="gd_discover_familial_relationships" name="Close relatives" version="1.0.0">
  <description>: Discover familial relationships</description>

  <command interpreter="python">
    #import json
    #import base64
    #import zlib
    #set $ind_names = $input.dataset.metadata.individual_names
    #set $ind_colms = $input.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)
    discover_familial_relationships.py '$input' '$input.ext' '$ind_arg' '$pop_input' '$output'
  </command>

  <inputs>
    <param name="input" type="data" format="gd_snp,gd_genotype" label="Input dataset" />
    <param name="pop_input" type="data" format="gd_indivs" label="Individuals dataset" />
  </inputs>

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

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

  <!--
  <tests>
  </tests>
  -->

  <help>

**Dataset formats**

The input datasets are in gd_snp_, gd_genotype_, and gd_indivs_ formats.
The output dataset is in tabular_ format.

.. _gd_snp: ./static/formatHelp.html#gd_snp
.. _gd_genotype: ./static/formatHelp.html#gd_genotype
.. _gd_indivs: ./static/formatHelp.html#gd_indivs
.. _tabular: ./static/formatHelp.html#tab

-----

**What it does**

The user specifies a SNP table (either gd_snp or gd_genotype format) and
a set of individuals.  The command runs the KING program (Manichaikul et
al., 2010) to look for pairs of distinct individuals in the specified
set that have a close family relationship.  Putatively related pairs
are classified into five categories:

  1. duplicate or MZ twin
  2. 1st degree relatives -- siblings (other than identical twins) or parent-child
  3. 2nd degree relatives -- e.g., half-siblings, grandparent-grandchild pair, individual-uncle/aunt pair
  4. 3rd degree relatives -- e.g., first cousins
  5. unrelated

Reference:

Manichaikul A, Mychaleckyj JC, Rich SS, Daly K, Sale M, Chen WM (2010) Robust relationship inference in genome-wide association studies. Bioinformatics 26: 2867-2873.
  </help>
</tool>