--- a/resize_coordinate_window.xml	Tue Jan 19 09:34:56 2016 -0500
+++ b/resize_coordinate_window.xml	Tue Feb 16 04:05:23 2016 -0500
@@ -1,21 +1,34 @@
-<tool id="resize_coordinate_window" name="Resize coordinate window" version="1.0.0">
+<tool id="resize_coordinate_window" name="Resize coordinate window" version="1.0.1">
     <description>of GFF data</description>
     <command>
         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" />
@@ -23,20 +36,43 @@
     <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 window size that is computed either from the existing start and end coordinates or centered on
+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**
@@ -47,7 +83,7 @@
     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::
+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`
@@ -57,7 +93,7 @@
     <citations>
         <citation type="bibtex">
             @unpublished{None,
-            author = {},
+            author = {Greg Von Kuster},
             title = {None},
             year = {None},
             eprint = {None},