<tool id="gd_specify" name="Specify Individuals" version="1.0.0">
  <description>: Define a collection of individuals from a gd_snp dataset</description>

  <command interpreter="bash">
    echo.bash "$input" "$output"
    #for $individual in str($individuals).split(',')
        #set $individual_idx = $input.dataset.metadata.individual_names.index($individual)
        #set $individual_col = str( $input.dataset.metadata.individual_columns[$individual_idx] )
        #set $arg = '\t'.join([$individual_col, $individual, ''])
        "$arg"
    #end for
  </command>

  <inputs>
    <param name="input" type="data" format="gd_snp" label="SNP dataset"/>
    <param name="individuals" type="select" display="checkboxes" multiple="true" label="Individuals to include">
      <options>
        <filter type="data_meta" ref="input" key="individual_names" />
      </options>
      <validator type="no_options" message="You must select at least one individual."/>
    </param>
    <param name="outname" type="text" size="20" label="Label for this collection">
      <validator type="empty_field" message="You must enter a label."/>
      #used to be "Individuals from ${input.hid}"
    </param>
  </inputs>

  <outputs>
    <data name="output" format="gd_indivs" label="${outname}" />
  </outputs>

  <tests>
    <test>
      <param name="input" value="test_in/sample.gd_snp" ftype="gd_snp" />
      <param name="individuals" value="PB1,PB2" />
      <output name="output" file="test_in/a.gd_indivs" />
    </test>
  </tests>

  <help>

**Dataset formats**

The input dataset is in gd_snp_ format;
the output is in gd_indivs_ 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**

This tool makes a list of selected entities (the sets of four columns
representing individuals or groups) from a gd_snp dataset.  It does not copy
the SNP data; it just records which entities should be considered as belonging
to some collection or population.  The label you specify is used to name the
output dataset in your history.  This list can then be used to instruct other
tools to work on just part of the original gd_snp dataset.

-----

**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.

- input metadata::

   #{"column_names":["scaf","pos","A","B","qual","ref","rpos","rnuc",
   #"1A","1B","1G","1Q","2A","2B","2G","2Q","3A","3B","3G","3Q","4A","4B","4G","4Q","5A","5B","5G","5Q","6A","6B","6G","6Q",
   #"pair","dist","prim","rflp"],"dbkey":"canFam2","individuals":[["PB1",9],["PB2",13],["PB3",17],["PB4",21],["PB6",25],["PB8",29]],
   #"pos":2,"rPos":7,"ref":6,"scaffold":1,"species":"bear"}

- output when individuals PB1, PB2, and PB3 are selected::

   9   PB1
   13  PB2
   17  PB3

  </help>
</tool>