<tool id="gd_inbreeding_and_kinship" name="Inbreeding and kinship" version="1.0.0">
  <description>: Analyze the pedigree without genomic data</description>

  <command interpreter="python">
    inbreeding_and_kinship.py '$ped_input' '$ind_input' '$computed_value' '$output'
    #if $kinship_dataset.choice == '0'
      '/dev/null'
    #else if $kinship_dataset.choice == '1'
      '$kinship_input'
    #end if
  </command>

  <inputs>
    <param name="ped_input" type="data" format="txt" label="Pedigree dataset" />
    <param name="ind_input" type="data" format="txt" label="Individuals dataset" />
    <conditional name="kinship_dataset">
      <param name="choice" type="select" format="integer" label="Kinship dataset">
        <option value="0" selected="true">no kinship dataset</option>
        <option value="1">select kinship dataset</option>
      </param>
      <when value="0" />
      <when value="1">
        <param name="kinship_input" type="data" format="txt" label="Kinship dataset" />
      </when>
    </conditional>
    <param name="computed_value" type="select" format="integer" label="Computed value">
      <option value="0" selected="true">inbreeding coeffiecients</option>
      <option value="1">kinships</option>
      <option value="2">mean kinships</option>
    </param>
  </inputs>

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

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

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

  <help>

**Dataset formats**

The input datasets are in text_ format.
The output dataset is in text_ format.

.. _text: ./static/formatHelp.html#text

-----

**What it does**

The user specifies a pedigree.  This is done with a Galaxy table with one
row per individual, containing (1) the individual's name, (2) the name of
one of the individual's parents, which must have occurred at the start
of a previous line, and (3) the name of the individual's other parent,
which occurred at the start of a previous line.  For a pedigree founder,
each parent name is replaced by &quot;-&quot;.

The user also provides a file that specifies a set of names of individuals
(specifically the first word on each line (one line per individual);
any subsequent information on a line is ignored.

The user can optionally provide a file giving kinship information for
each pair of distinct individuals from the founder set.

Finally the user picks from among the options:

  1. inbreeding coefficients for each specified individual
  2. the kinship for each pair of distinct specified individual
  3. the mean kinship for each specified individual, i.e., the average kinship value for that individual and every specified individual

The command reports the requested values.

-----

**Example**

- input::

   A - -
   B - -
   C - -
   D - -
   E - -
   F A B
   G A B
   Thelma A F
   Louise F G

Rows can have more than three columns (such as the individual's sex),
but only the first three columns affect this command.

Suppose on the other hand that we select an alternative
&quot;founder&quot; set, {A, F, G}.  (We require a founder sets to have a
member on any ancestral path from Thelma or Louise.)  The above pedigree
file is then replaced by::

   A - -
   F - -
   G - -
   Thelma A F
   Louise F G

The user then also provides a file giving kinship information for each
pairs of distinct individuals from the founder set; for the current
example, the kinship file is as follows::

   A F 0.25
   A G 0.25
   F G 0.25

since parent-child pairs and siblings both have kinship 0.25.  The
advantage is that this capability can be used in cases where the kinships
of the founders are not initially known, but instead are computationally
predicted, e.g., with the Galaxy &quot;Discover&quot; tool.
  </help>
</tool>