<tool id="gd_dpmix" name="Admixture" version="1.1.0">
  <description>: Map genomic intervals resembling specified ancestral populations</description>

  <command interpreter="python">
    dpmix.py "$input"
    #if $input_type.choice == '0'
      "gd_snp" "$input_type.data_source"
    #else if $input_type.choice == '1'
      "gd_genotype" "1"
    #end if
    "$switch_penalty" "$ap1_input" "$ap2_input" "$p_input" "$output" "$output2" "$output2.files_path" "$input.dataset.metadata.dbkey" "$input.dataset.metadata.ref" "$GALAXY_DATA_INDEX_DIR" "gd.heterochromatic.loc"
    #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">
          <validator type="unspecified_build" message="This dataset does not have a reference species and cannot be used with this tool" />
        </param>

        <param name="data_source" type="select" format="integer" label="Similarity metric">
          <option value="0">sequence coverage</option>
          <option value="1" selected="true">estimated genotype</option>
        </param>
      </when>
      <when value="1">
        <param name="input" type="data" format="gd_genotype" label="Genotype dataset">
          <validator type="unspecified_build" message="This dataset does not have a reference species and cannot be used with this tool" />
        </param>
      </when>
    </conditional>

    <param name="ap1_input" type="data" format="gd_indivs" label="Ancestral population 1 individuals" />
    <param name="ap2_input" type="data" format="gd_indivs" label="Ancestral population 2 individuals" />
    <param name="p_input" type="data" format="gd_indivs" label="Potentially admixed individuals" />

    <param name="switch_penalty" type="integer" min="0" value="10" label="Genotype switch penalty" help="Note: typically between 10 and 100."/>
  </inputs>

  <outputs>
    <data name="output" format="tabular" />
    <data name="output2" format="html" />
  </outputs>

  <tests>
    <test>
      <param name="input" value="test_in/sample.gd_snp" ftype="gd_snp" />
      <param name="ap1_input" value="test_in/a.gd_indivs" ftype="gd_indivs" />
      <param name="ap2_input" value="test_in/b.gd_indivs" ftype="gd_indivs" />
      <param name="p_input" value="test_in/c.gd_indivs" ftype="gd_indivs" />
      <param name="data_source" value="0" />
      <param name="switch_penalty" value="10" />

      <output name="output" file="test_out/dpmix/dpmix.tabular" />

      <output name="output2" file="test_out/dpmix/dpmix.html" ftype="html" compare="diff" lines_diff="2">
        <extra_files type="file" name="dpmix.pdf" value="test_out/dpmix/dpmix.pdf" compare="sim_size" delta = "10000" />
        <extra_files type="file" name="misc.txt" value="test_out/dpmix/misc.txt" />
      </output>
    </test>
  </tests>

  <help>

**Dataset formats**

The input datasets are in gd_snp_, gd_genotype_, and gd_indivs_ formats.  It is important for
the Individuals datasets to have unique names and for there to be no overlap
between the two populations.  Rename these datasets if
needed to make them unique.  
There are two output datasets, one tabular_ and one composite. (`Dataset missing?`_)

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

-----

**What it does**

The user specifies two "ancestral" populations (i.e., sources for
chromosomes) and a set of potentially admixed individuals, and chooses
between the sequence coverage or the estimated genotypes to measure
the similarity of genomic intervals in admixed individuals to the two
classes of ancestral chromosomes.  The user also picks a "genotype switch penalty",
typically between 10 and 100.  For each potentially admixed individual,
the program divides the genome into three "genotypes": (0) homozygous
for the first ancestral population (i.e., both chromosomes from that
population), (1) heterozygous, or (2) homozygous for the second ancestral
population.  Parts of a chromosome that are labeled as "heterochromatic"
are given the non-genotype "3".  Smaller values of the switch penalty
(corresponding to more ancient admixture events) generally lead to the
reconstruction of more frequent changes between genotypes.

There are two output datasets generated.  A tabular dataset with chromosome,
start, stop, and pairs of columns containing the "genotypes" from above
and label from the admixed individual.  The second dataset is a composite
dataset with general information from the run and a link to a pdf which
graphically shows the ancestral population along each of the chromosomes.
The second link is to a text file with summary information of the 
"genotypes" over the whole genome.

  </help>
</tool>