annotate aggregate_gd_indivs.xml @ 26:91e835060ad2

Updates to Admixture, Aggregate Individuals, and Restore Attributes to support gd_genotype

<tool id="gd_sum_gd_snp" name="Aggregate Individuals" version="1.1.0">
  <description>: Append summary columns for a population</description>

  <command interpreter="python">
    aggregate_gd_indivs.py "$input" "$p1_input" "$output"
    #if $input_type.choice == '0'
      "gd_snp"
    #else if $input_type.choice == '1'
      "gd_genotype"
    #end if
    #for $individual, $individual_col in zip($input.dataset.metadata.individual_names, $input.dataset.metadata.individual_columns)
        #set $arg = '%s:%s' % ($individual_col, $individual)
        "$arg"
    #end for
  </command>

  <inputs>

  <conditional name="input_type">
    <param name="choice" type="select" format="integer" label="Input format">
      <option value="0" selected="true">gd_snp</option>
      <option value="1">gd_genotype</option>
    </param>

    <when value="0">
      <param name="input" type="data" format="gd_snp" label="SNP dataset" />
    </when>
    <when value="1">
      <param name="input" type="data" format="gd_genotype" label="Genotype dataset" />
    </when>
  </conditional>

    <param name="p1_input" type="data" format="gd_indivs" label="Population individuals" />
  </inputs>

  <outputs>
    <data name="output" format="input" format_source="input" metadata_source="input" />
  </outputs>

  <tests>
    <test>
      <param name="input" value="test_in/sample.gd_snp" ftype="gd_snp" />
      <param name="p1_input" value="test_in/a.gd_indivs" ftype="gd_indivs" />
      <output name="output" file="test_out/modify_snp_table/modify.gd_snp" />
    </test>
  </tests>

  <help>

**Dataset formats**

The input datasets are in gd_snp_, gd_genotype_, and gd_indivs_ formats.
The output dataset is in gd_snp_ or gd_genotype_ format.  (`Dataset missing?`_)

.. _gd_snp: ./static/formatHelp.html#gd_snp
.. _gd_genotype: ./static/formatHelp.html#gd_genotype
.. _gd_indivs: ./static/formatHelp.html#gd_indivs
.. _Dataset missing?: ./static/formatHelp.html

-----

**What it does**

The user specifies that some of the individuals in a gd_snp or gd_genotype
dataset form a "population", by supplying a list that has been previously
created using the Specify Individuals tool.  The program appends a new
"entity" (set of four columns for a gd_snp table, or one column for a
gd_genotype table), analogous to the column(s) for an individual but
containing summary data for the population as a group.  For a gd_snp
table, these four columns give the total counts for the two alleles,
the "genotype" for the population, and the maximum quality value, taken
over all individuals in the population.  If all defined genotypes in
the population are 2 (agree with the reference), then the population's
genotype is 2, and similarly for 0; otherwise the genotype is 1 (unless
all individuals have undefined genotype, in which case it is -1).
For a gd_genotype file, only the aggregate genotype is appended.

-----

**Example**

- input gd_snp::

    Contig161_chr1_4641264_4641879   115  C  T  73.5   chr1   4641382  C   6  0  2  45   8  0  2  51   15  0  2  72   5  0  2  42   6  0  2  45   10  0  2  57   Y  54  0.323  0
    Contig48_chr1_10150253_10151311   11  A  G  94.3   chr1  10150264  A   1  0  2  30   1  0  2  30    1  0  2  30   3  0  2  36   1  0  2  30    1  0  2  30   Y  22  +99.   0
    Contig20_chr1_21313469_21313570   66  C  T  54.0   chr1  21313534  C   4  0  2  39   4  0  2  39    5  0  2  42   4  0  2  39   4  0  2  39    5  0  2  42   N   1  +99.   0
    etc.

- input individuals::

    9   PB1
    13  PB2
    17  PB3

- output::

    Contig161_chr1_4641264_4641879   115  C  T  73.5   chr1   4641382  C   6  0  2  45   8  0  2  51   15  0  2  72   5  0  2  42   6  0  2  45   10  0  2  57   Y  54  0.323  0   29  0  2  72
    Contig48_chr1_10150253_10151311   11  A  G  94.3   chr1  10150264  A   1  0  2  30   1  0  2  30    1  0  2  30   3  0  2  36   1  0  2  30    1  0  2  30   Y  22  +99.   0    3  0  2  30
    Contig20_chr1_21313469_21313570   66  C  T  54.0   chr1  21313534  C   4  0  2  39   4  0  2  39    5  0  2  42   4  0  2  39   4  0  2  39    5  0  2  42   N   1  +99.   0   13  0  2  42
    etc.

  </help>
</tool>