<tool id="gd_prepare_population_structure" name="Prepare" version="1.0.0">
  <description>to look for population structure</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 table" />
    <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>
**What it does**

The tool converts a SNP table 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" after the program runs.
  </help>
</tool>