<tool id="gd_sum_gd_snp" name="Aggregate Individuals" version="1.0.0">
  <description>: Append summary columns for a population</description>

  <command interpreter="python">
    modify_snp_table.py "$input" "$p1_input" "$output" "-1" "-1" "-1" "-1"
    #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>
    <param name="input" type="data" format="gd_snp" label="SNP dataset" />
    <param name="p1_input" type="data" format="gd_indivs" label="Population individuals" />
  </inputs>

  <outputs>
    <data name="output" format="gd_snp" 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" />
      <param name="choice" value="1" />
      <param name="lo_coverage" value="0" />
      <param name="hi_coverage" value="1000" />
      <param name="low_ind_cov" value="3" />
      <param name="lo_quality" value="30" />
      <output name="output" file="test_out/modify_snp_table/modify.gd_snp" />
    </test>
  </tests>

  <help>

**Dataset formats**

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

.. _gd_snp: ./static/formatHelp.html#gd_snp
.. _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 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) to the gd_snp table, analogous to the columns
for an individual but containing summary data for the population as a group.
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).

-----

**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>