<tool id="resize_coordinate_window" name="Resize coordinate window" version="1.0.0">
    <description>of GFF data</description>
    <command>
        python $__tool_directory__/resize_coordinate_window.py
        --input "$input"
        --subtract_from_start $subtract_from_start
        --add_to_end $add_to_end
        --extend_existing $extend_existing
        --output "$output"
    </command>
    <inputs>
        <param name="input" type="data" format="gff" label="Gff file" />
        <param name="subtract_from_start" type="integer" value="30" min="0" label="Distance to subtract from the start coordinate"/>
        <param name="add_to_end" type="integer" value="30" min="0" label="Distance to add to the end coordinate"/>
        <param name="extend_existing" type="select" label="Resize window from" help="The midpoint is computed as (start + end) // 2">
            <option value="midpoint" selected="True">the midpoint of the start and end coordinates</option>
            <option value="existing">the start and end coordinates</option>
        </param>
    </inputs>
    <outputs>
        <data name="output" format="gff" />
    </outputs>
    <tests>
        <test>
            <param name="input" value="input.gff" ftype="gff" />
            <param name="subtract_from_start" value="13" />
            <param name="add_to_end" value="13" />
            <param name="extend_existing" value="midpoint" />
            <output name="output" file="output.gff" ftype="gff" />
        </test>
    </tests>
    <help>

**What it does**

Modifies the start and end coordinates of GFF data such that the new start and end position is based on a
specified window size that is computed either from the existing start and end coordinates or centered on
the midpoint between them.

-----

**Example**

If the input dataset is::

    chr1    genetrack       .       17      37      918     +       .       stddev=5.96715849116
    chr1    genetrack       .       31      51      245     -       .       stddev=2.66582799529
    chr1    genetrack       .       40      60      2060    +       .       stddev=2.7859667372

Resizing the coordinate window by 13 from the computed midpoint of the start and end coordinates produces::

    chr1    genetrack       .       14      40      918     +       .       stddev=5.96715849116
    chr1    genetrack       .       28      54      245     -       .       stddev=2.66582799529`
    chr1    genetrack       .       37      63      2060    +       .       stddev=2.7859667372

    </help>
    <citations>
        <citation type="bibtex">
            @unpublished{None,
            author = {},
            title = {None},
            year = {None},
            eprint = {None},
            url = {http://www.huck.psu.edu/content/research/independent-centers-excellence/center-for-eukaryotic-gene-regulation}
        }</citation>
    </citations>
</tool>