<tool id="gd_select_individuals" name="Select individuals" version="1.0.0">
  <description>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="gd_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>
  </inputs>

  <outputs>
    <data name="output" format="gd_indivs" label="Individuals from ${input.hid}" />
  </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 the gd_snp_ format.
The output dataset is in gd_indivs_ format.  (`Dataset missing?`_)

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

**What it does**

This selects a set of individuals or groups from a gd_snp dataset.   This set
can then be used by other tools to work on just part of the gd_snp dataset.

**Examples**

- 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>