--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/gemini_windower.xml	Mon Aug 25 17:15:54 2014 -0400
@@ -0,0 +1,64 @@
+<tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0">
+    <description>Conducting analyses on genome "windows"</description>
+    <expand macro="requirements" />
+    <expand macro="version_command" />
+    <macros>
+        <import>gemini_macros.xml</import>
+        <token name="@BINARY@">windower</token>
+    </macros>
+    <command>
+<![CDATA[
+        gemini @BINARY@
+            -w $w
+            -s $s
+            -t $window_analysis
+            -o $operation
+            "${ infile }"
+            > "${ outfile }"
+]]>
+    </command>
+    <expand macro="stdio" />
+    <inputs>
+        <param name="infile" type="data" format="sqlite" label="GEMINI database" />
+
+        <param name="window_analysis" type="select" label="The type of window analysis requested?" help="(-t)">
+            <option value="nucl_div">(nucl_div)</option>
+            <option value="hwe">(hwe)</option>
+        </param>
+
+        <param name="operation" type="select" label="The operation that should be applied to the -t values" help="(-o)">
+            <option value="mean">mean</option>
+            <option value="median">median</option>
+            <option value="min">min</option>
+            <option value="max">max</option>
+            <option value="collapse">collapse</option>
+        </param>
+
+        <param name="w" type="integer" value="10000" size="10" label="The window size in bp" 
+            help="(-w)">
+            <validator type="in_range" min="0"/>
+        </param>
+
+        <param name="s" type="integer" value="1000" size="10" label="The step size for the windows in bp" 
+            help="(-s)">
+            <validator type="in_range" min="0"/>
+        </param>
+
+    </inputs>
+
+    <outputs>
+        <data name="outfile" format="tabular" label="${tool.name} on ${on_string}" />
+    </outputs>
+    <tests>
+        <test>
+        </test>
+    </tests>
+    <help>
+**What it does**
+
+It computs variation metrics across genomic windows (both fixed and sliding).
+
+@CITATION@
+    </help>
+    <expand macro="citations"/>
+</tool>