--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/resize_coordinate_window.xml	Tue Jan 19 09:34:56 2016 -0500
@@ -0,0 +1,67 @@
+<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>