<tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0">
    <description>Conducting analyses on genome "windows"</description>
    <macros>
        <import>gemini_macros.xml</import>
        <token name="@BINARY@">windower</token>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <expand macro="version_command" />
    <command>
<![CDATA[
        gemini @BINARY@
            -w $w
            -s $s
            -t $window_analysis
            -o $operation
            "${ infile }"
            > "${ outfile }"
]]>
    </command>
    <inputs>
        <expand macro="infile" />

        <param name="window_analysis" type="select" label="The type of window analysis requested?" help="(-t)">
            <option value="nucl_div">(nucl_div)</option>
            <option value="hwe">(hwe)</option>
        </param>

        <param name="operation" type="select" label="The operation that should be applied to the -t values" help="(-o)">
            <option value="mean">mean</option>
            <option value="median">median</option>
            <option value="min">min</option>
            <option value="max">max</option>
            <option value="collapse">collapse</option>
        </param>

        <param name="w" type="integer" value="10000" label="The window size in bp"
            help="(-w)">
            <validator type="in_range" min="0"/>
        </param>

        <param name="s" type="integer" value="1000" label="The step size for the windows in bp"
            help="(-s)">
            <validator type="in_range" min="0"/>
        </param>

    </inputs>

    <outputs>
        <data name="outfile" format="tabular" />
    </outputs>
    <tests>
        <test>
            <param name="infile" value="gemini_windower_input.db" ftype="gemini.sqlite" />
            <param name="w" value="10000" />
            <param name="window_analysis" value="nucl_div" />
            <param name="operation" value="mean" />
            <output name="outfile" file="gemini_windower_result.tabular" />
        </test>
    </tests>
    <help><![CDATA[
**What it does**

It computs variation metrics across genomic windows (both fixed and sliding).

**Examples**

Compute the average nucleotide diversity for all variants found in non-overlapping, 50Kb windows with following settings::

 -w 50000 
 -s 0 
 -t nucl_div 
 -o mean

Compute the average nucleotide diversity for all variants found in 50Kb windows that overlap by 10kb with following settings::

 -w 50000
 -s 10000
 -t nucl_div
 -o mean 

Compute the max value for HWE statistic for all variants in a window of size 10kb with following settings::

 -w 10000 
 -t hwe
 -o max

    ]]></help>
    <expand macro="citations"/>
</tool>