<tool id="gd_specify" name="Specify Individuals" version="1.1.0">
  <description>: Define a collection of individuals from a gd_snp dataset</description>

  <command interpreter="python">
    specify.py "$input" "$output"
    #for $individual, $individual_col in zip($input.dataset.metadata.individual_names, $input.dataset.metadata.individual_columns)
      #set $individual_arg = 'individual:%s:%s' % ($individual_col, $individual)
      "$individual_arg"
    #end for
    #if str($individuals).strip() != 'None'
        #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 $cb_arg = 'checkbox:%s:%s' % ($individual_col, $individual)
          "$cb_arg"
        #end for
    #end if
    #if str($string).strip() != ''
      #set str_arg = 'string:%s' % ( __import__('base64').b64encode( str($string) ) )
      "$str_arg"
    #end if
  </command>

  <inputs>
    <param name="input" type="data" format="gd_snp,gd_genotype" label="SNP or Genotype 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>
    </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>
    <param name="string" type="text" size="40" label="Individuals to include">
      <sanitizer>
        <valid initial="string.printable"/>
      </sanitizer>
    </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_ or gd_genotype_ format;
the output is in gd_indivs_ format.  (`Dataset missing?`_)

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

-----

**What it does**

This tool makes a list of selected entities, i.e., the sets of four
columns representing individuals or groups from a gd_snp dataset, or
sets of single columns in a gd_genotype file.  It does not copy the
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 or
gd_genotype dataset.  The entities can be specified with the checklist
and/or by pasting their names (possibly with extraneous characters, as
in a portion of the Newick-format output of the Phylogenetic Tree tool)
into the box provided at the bottom of the page.

-----

**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>