<tool id="bg_uniq" name="Unique" version="0.3">
  <description>occurrences of each record</description>
  <command interpreter='python'>
    unique_lines.py 
        $ignore_case 
        $is_numeric
        #if $adv_opts.adv_opts_selector=="advanced":
            $adv_opts.column_start
            $adv_opts.column_end
        #end if
        $outfile
        $input
  </command>
  <inputs>
    <param name="input" type="data" format="tabular,text" label="from query" /> 
    <param name="ignore_case" type="boolean" label="ignore differences in case when comparing" truevalue="-f" falsevalue="false" checked="false" help="ignore differences in case when comparing"/>
    <param name="is_numeric" type="boolean" label="column only contains numeric values" truevalue="-n" falsevalue="false" checked="false" help="did the calumn have numeric values"/>
    <conditional name="adv_opts">
        <param name="adv_opts_selector" type="select" label="Advanced Options">
          <option value="basic" selected="True">Hide Advanced Options</option>
          <option value="advanced">Show Advanced Options</option>
        </param>
        <when value="basic" />
        <when value="advanced">
            <param name="column_start" label="Column start" type="data_column" data_ref="input" help="Unique on specific column range"/>
            <param name="column_end" label="Column end" type="data_column" data_ref="input" help="Unique on specific column range"/>
        </when>
    </conditional>
  </inputs>
  <outputs>
    <data format="input" name="outfile" />
  </outputs>
  <tests>
    <test>
    </test>
  </tests>
  <help>
  
 .. class:: infomark

**Syntax**

This tool returns all unique lines using the 'sort -u' command.

-----

.. class:: infomark

The input file needs to be tab separated. Please convert your file if necessary.

-----

**Example**

- Input file::
     
       chr1   10  100  gene1
       chr1  105  200  gene2
       chr1   10  100  gene1
       chr2   10  100  gene4
       chr2 1000 1900  gene5
       chr3   15 1656  gene6
       chr2   10  100  gene4

- Unique lines will result in::

       chr1   10  100  gene1
       chr1  105  200  gene2
       chr2   10  100  gene4
       chr2 1000 1900  gene5
       chr3   15 1656  gene6


</help>
</tool>