--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/gemini_windower.xml	Thu Feb 18 08:52:15 2016 -0500
@@ -0,0 +1,90 @@
+<tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0">
+    <description>Conducting analyses on genome "windows"</description>
+    <macros>
+        <import>gemini_macros.xml</import>
+        <token name="@BINARY@">windower</token>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="stdio" />
+    <expand macro="version_command" />
+    <command>
+<![CDATA[
+        gemini @BINARY@
+            -w $w
+            -s $s
+            -t $window_analysis
+            -o $operation
+            "${ infile }"
+            > "${ outfile }"
+]]>
+    </command>
+    <inputs>
+        <expand macro="infile" />
+
+        <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" label="The window size in bp"
+            help="(-w)">
+            <validator type="in_range" min="0"/>
+        </param>
+
+        <param name="s" type="integer" value="1000" 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" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="infile" value="gemini_windower_input.db" ftype="gemini.sqlite" />
+            <param name="w" value="10000" />
+            <param name="window_analysis" value="nucl_div" />
+            <param name="operation" value="mean" />
+            <output name="outfile" file="gemini_windower_result.tabular" />
+        </test>
+    </tests>
+    <help><![CDATA[
+**What it does**
+
+It computs variation metrics across genomic windows (both fixed and sliding).
+
+**Examples**
+
+Compute the average nucleotide diversity for all variants found in non-overlapping, 50Kb windows with following settings::
+
+ -w 50000 
+ -s 0 
+ -t nucl_div 
+ -o mean
+
+Compute the average nucleotide diversity for all variants found in 50Kb windows that overlap by 10kb with following settings::
+
+ -w 50000
+ -s 10000
+ -t nucl_div
+ -o mean 
+
+Compute the max value for HWE statistic for all variants in a window of size 10kb with following settings::
+
+ -w 10000 
+ -t hwe
+ -o max
+
+    ]]></help>
+    <expand macro="citations"/>
+</tool>