--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/alignvis.xml	Sat Mar 10 07:59:27 2012 -0500
@@ -0,0 +1,42 @@
+<tool id="alignvis" name="heatmap">
+  <description>of align output</description>
+  <command interpreter="python"> alignvis.py $input $output $uselog $subset $reorder $color $scale </command>
+  <inputs>
+    <param name="input" format="tabular" type="data" label="Original file"/>
+    <param name="uselog" label="log transform the data" type="boolean" truevalue="uselog" falsevalue="none" checked="True"/>
+    <param name="subset" label="sample a subset if the data is too large" type="boolean" truevalue="subset" falsevalue="none" checked="True"/>
+    <param name="scale" label="normalize by row/feature" type="boolean" truevalue="scale" falsevalue="none" checked="False"/>
+    <param name="reorder" type="select" label="reorder features (rows)">
+      <option value="none" selected="true">None</option>
+      <option value="sort_by_sum">Sort row by sum</option>
+      <option value="sort_by_center">Sort row by center </option>
+      <option value="average">Cluster rows (average)</option>    
+      <option value="median">Cluster rows (median) </option>    
+      <option value="centroid">Cluster rows (centroid)</option>    
+      <option value="complete">Cluster rows (complete)</option>    
+      <option value="single">Cluster rows (single)</option> 
+          </param>
+             
+    <param name="color" type="select" label="color scheme">
+    <option value="heat" selected="true">heat</option>
+    <option value="gray">gray</option>
+    <option value="rainbow">rainbow</option>    
+    <option value="topo">topo</option>    
+    <option value="terrain">terrain</option>    
+    </param>
+  </inputs>
+  <outputs>
+    <data format="pdf" name="output" />
+  </outputs>
+  <help>
+
+**What it does**
+
+This tool generates a heatmap for output from 'align' tool. Each row is the color-coded coverage of a feature, and the features are sorted by the total coverage in the interval.  
+
+**Example**
+
+.. image:: ./static/operation_icons/heatmap.png
+
+  </help>
+</tool>