annotate offspring_heterozygosity.xml @ 32:03c22b722882

remove BeautifulSoup dependency

<tool id="gd_offspring_heterozygosity" name="Pairs sequenced" version="1.0.0">
  <description>: Offspring estimated heterozygosity of sequenced pairs</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.py '$input' '$input.ext' '$ind_arg' '$p1_input' '$p2_input' '$output'
  </command>

  <inputs>
    <param name="input" type="data" format="gd_snp,gd_genotype" label="SNP dataset" />
    <param name="p1_input" type="data" format="gd_indivs" label="First individuals dataset" />
    <param name="p2_input" type="data" format="gd_indivs" label="Second individuals 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_, 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**

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.  In other words, we add the following numbers for
each autosomal SNP where both genotypes are defined, then divide by the
number of those SNPs:

0 if the individuals are homozygous for the same nucleotide

1 if the individuals are homozygous for different nucleotides

1/2 otherwise (i.e., if one or both individuals are heterozygous) 

A SNP is ignored if one or both individuals have an undefined genotype
(designated as -1).
  </help>
</tool>