<tool id="resize_coordinate_window" name="Resize coordinate window" version="1.0.1">
    <description>of GFF data</description>
    <command detect_errors="exit_code"><![CDATA[
python '$__tool_directory__/resize_coordinate_window.py'
--input '$input'
--start_coordinate $start_coordinate
--subtract_from_start $subtract_from_start
--add_to_end $add_to_end
--extend_existing $extend_existing
--chrom_len_file '${chromInfo}'
--region_boundaries $region_boundaries
--output '$output'
    ]]></command>
    <inputs>
        <param name="input" type="data" format="gff" label="Gff file" />
        <param name="start_coordinate" type="select" label="Start coordinate" help="Input data is 0-based or 1-based">
            <option value="0" selected="True">0</option>
            <option value="1">1</option>
        </param>
        <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>
        <param name="region_boundaries" type="select" label="Handle chromosome boundaries by" help="Expanding the region may result in crossing chromosome start and end coordinate boundaries.">
            <option value="discard" selected="True">discarding the region</option>
            <option value="limit">keeping the region by limiting the expansion to not cross the start or end coordinate boundary</option>
            <option value="nothing">keeping the region by allowing the expansion to cross the start or end coordinate boundary</option>
            <option value="error">outputting an error</option>
        </param>
    </inputs>
    <outputs>
        <data name="output" format="gff" />
    </outputs>
    <tests>
        <test>
            <param name="input" value="input.gff" ftype="gff" />
            <param name="start_coordinate" value="1" />
            <param name="subtract_from_start" value="13" />
            <param name="add_to_end" value="13" />
            <param name="extend_existing" value="midpoint" />
            <param name="region_boundaries" value="error" />
            <output name="output" file="output.gff" ftype="gff" />
        </test>
        <test>
            <param name="input" value="input.gff" ftype="gff" />
            <param name="start_coordinate" value="0" />
            <param name="subtract_from_start" value="80" />
            <param name="add_to_end" value="80" />
            <param name="extend_existing" value="midpoint" />
            <param name="region_boundaries" value="discard" />
            <output name="output" file="output_discard.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 region size that is computed either from the existing start and end coordinates or centered on
the midpoint between them.

Region expansion may result in the new start or end coordinates crossing the chromosome boundary.  The
chromosome start is set to 0 or 1 using the **Start coordinate** parameter.  The end is retrieved from a
file within the Galaxy environment that includes the length of chromosomes for all genome builds.  If these
files are missing, the end coordinate is set to 2147483647, which is the maximum value of a signed 32 bit
integer.  The **Handle chromosome boundaries by** parameter handles chromosome boundaries that are crossed
by expanding the region using one of the following options.

* **discarding the region** - the region will be discarded and processing will continue with the next line in the dataset.
* **keeping the region by limiting the expansion to not cross the start or end coordinate boundary** - expansion will be restricted to not cross the chromosome's start or end coordinates for the current region.
* **keeping the region by allowing the expansion to cross the start or end coordinate boundary** - allow defined expansion, crossing the start boundary results in a negative start value.
* **outputting an error** - Stop processing and display an error.

-----

**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

Setting start coordinate to 1 and 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 = {Greg Von Kuster},
            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>