<tool id="gd_offspring_heterozygosity_pedigree" name="Founders sequenced" version="1.0.0">
  <description>: Offspring estimated heterozygosity from a pedigree with sequenced founders</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)
    offspring_heterozygosity_pedigree.py '$input' '$input.ext' '$pedigree' '$ind_arg' '$founders' '$b1_input' '$b2_input' '$output'
  </command>

  <inputs>
    <param name="input" type="data" format="gd_snp,gd_genotype" label="SNP dataset" />
    <param name="pedigree" type="data" format="txt" label="Pedigree dataset" />
    <param name="founders" type="data" format="gd_indivs" label="Founders dataset" />
    <param name="b1_input" type="data" format="txt" label="First breeders dataset" />
    <param name="b2_input" type="data" format="txt" label="Second breeders dataset" />
  </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 gd_snp_, gd_genotype_, text_, and gd_indivs_ formats.
The output dataset is in text_ format.

.. _gd_snp: ./static/formatHelp.html#gd_snp
.. _gd_genotype: ./static/formatHelp.html#gd_genotype
.. _gd_indivs: ./static/formatHelp.html#gd_indivs
.. _text: ./static/formatHelp.html#text

-----

**What it does**

The user provides a Galaxy SNP table (gd_snp or gd_genotype format) that
includes the founders of a pedigree, as well as two sets of individuals.
The pedigree is specified by a text file 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, both parent names
are replaced by &quot;-&quot;.  The founders are specified by a table in
gd_indivs format, e.g., as produced by &quot;Specify individuals&quot;
tool.  Every founder must have genotypes supplied in the SNP table,
and both parents need to be given as &quot;-&quot; in the pedigree.
Conversely, every pedigree individual whose parents are &quot;-&quot;
must be named as a founder.

The user also provides two files that specify a set of names of
individuals.  The first word on each line names an individual (one
line per individual); any subsequent information on a line is ignored.
The name of each individual must appear at the start of a line in the
pedigree.

For each pair of individuals, one from each specified set, the program
computes the expected heterozygosity of any offspring of the pair,
i.e., the probability that the offspring has distinct nucleotides at
a randomly chosen autosomal SNP.  A SNP is ignorned if one or both
potential parents have an ancestor with undefined genotype (designated
as -1 in the SNP table).
  </help>
</tool>