<tool id="gd_prepare_population_structure" name="Prepare Input" version="1.0.0">
  <description>: Filter and convert to the format needed for these tools</description>

  <command interpreter="python">
    prepare_population_structure.py "$input" "$min_reads" "$min_qual" "$min_spacing" "$output" "$output.files_path"
    #if $individuals.choice == '0'
        "all_individuals"
    #else if $individuals.choice == '1'
        #for $population in $individuals.populations
          #set $pop_arg = 'population:%s:%s' % (str($population.p_input), str($population.p_input.name))
          "$pop_arg"
        #end for
    #end if
    #for $individual, $individual_col in zip($input.dataset.metadata.individual_names, $input.dataset.metadata.individual_columns)
        #set $arg = 'individual:%s:%s' % ($individual_col, $individual)
        "$arg"
    #end for
  </command>

  <inputs>
    <param name="input" type="data" format="gd_snp" label="SNP dataset" />
    <param name="min_reads" type="integer" min="0" value="0" label="Minimum reads covering a SNP, per individual" />
    <param name="min_qual" type="integer" min="0" value="0" label="Minimum quality value, per individual" />
    <param name="min_spacing" type="integer" min="0" value="0" label="Minimum spacing between SNPs on the same scaffold" />
    <conditional name="individuals">
      <param name="choice" type="select" label="Individuals">
        <option value="0" selected="true">All</option>
        <option value="1">Choose</option>
      </param>
      <when value="0" />
      <when value="1">
        <repeat name="populations" title="Population" min="1">
          <param name="p_input" type="data" format="gd_indivs" label="Individuals" />
        </repeat>
      </when>
    </conditional>
  </inputs>

  <outputs>
    <data name="output" format="gd_ped">
      <actions>
        <action type="metadata" name="base_name" default="admix" />
      </actions>
    </data>
  </outputs>

  <tests>
    <test>
      <param name="input" value="test_in/sample.gd_snp" ftype="gd_snp" />
      <param name="min_reads" value="3" />
      <param name="min_qual" value="30" />
      <param name="min_spacing" value="0" />
      <param name="choice" value="0" />
      <output name="output" file="test_out/prepare_population_structure/prepare_population_structure.html" ftype="html" compare="diff" lines_diff="2">
        <extra_files type="file" name="admix.map" value="test_out/prepare_population_structure/admix.map" />
        <extra_files type="file" name="admix.ped" value="test_out/prepare_population_structure/admix.ped" />
      </output>
    </test>
  </tests>

  <help>

**Dataset formats**

The input datasets are in gd_snp_ and gd_indivs_ formats.  It is important
for the Individuals datasets to have unique names; rename them if
necessary to make them unique.  These names are used by the later tools in
the graphical displays.
The output dataset is gd_ped_.  (`Dataset missing?`_)

.. _gd_snp: ./static/formatHelp.html#gd_snp
.. _gd_indivs: ./static/formatHelp.html#gd_indivs
.. _gd_ped: ./static/formatHelp.html#gd_ped
.. _Dataset missing?: ./static/formatHelp.html

-----

**What it does**

The tool converts a gd_snp dataset into two tables, called "admix.map" and
"admix.ped", needed for estimating the population structure.  The user
can read or download those files, or simply pass this tool's output on to
other programs.  The user imposes conditions on which SNPs to consider,
such as the minimum coverage and/or quality value for every individual,
or the distance to the closest SNP in the same contig (as named in the
first column of the SNP table).  A useful piece of information produced
by the tool is the number of SNPs meeting those conditions, which can
be found by clicking on the eye icon in the history panel after the program 
runs.

-----

**Example**

- input::

    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.

- output map file::

    1 snp1 0 2
    1 snp3 0 4
    1 snp4 0 5
    1 snp5 0 6
    1 snp6 0 7
    1 snp7 0 8
    1 snp8 0 9
    1 snp9 0 10

- output ped file::

    PB1 1 0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1

  </help>
</tool>