--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mytools/bwBinavg.xml	Fri Mar 09 20:01:43 2012 -0500
@@ -0,0 +1,44 @@
+<tool id="bwbinavg" name="bigwig summary">
+  <description>for intervals</description>
+  <command interpreter="python">getGenomicScore.py $input $output $score_type $bwfile $nbin $strand $outplot $span</command>
+  <inputs>
+      <param name="input" format="interval" type="data" label="Interval file"/>
+      <param name="bwfile" format="bigwig" type="data" label="BigWig file"/>
+      <param name="score_type" type="select" label="Select score summary type" >
+		  <option value="mean" selected="true">mean</option>
+		  <option value="max">maximum</option>
+		  <option value="min">minimum</option>
+		  <option value="std">standard deviation</option>
+		  <option value="coverage">coverage:fraction covered</option>
+      </param>
+      <param name="nbin" type="integer" value="1" label="number of bins"/>          
+        <param name="strand" type="integer" value="0" label="Specify the strand column" help="leave 0 to ignore strand information. Only matters if using more than 1 bin"/>   
+        <param name="span" size="10" type="float" value="0.1" label="loess span: smoothing parameter" help="value less then 0.1 disables smoothing"/>
+  </inputs>
+  <outputs>
+     <data format="pdf" name="outplot" label="${tool.name} on ${on_string}[plot]"/>
+    <data format="interval" name="output" label="${tool.name} on ${on_string}[data]"/>
+  </outputs>
+  <help>
+
+.. class:: infomark
+
+Each interval is binned and the average base-resolution score/coverage/density in the bigwig file is added as new columns appended at the end of the original file .
+
+**Example**
+
+If your original data has the following format:
+
++-----+-----+---+------+
+|chrom|start|end|other2|
++-----+-----+---+------+
+
+and you choose to divide each interval into 3 bins and return the mean scores of each bin, your output will look like this:
+
++-----+-----+---+------+-----+-----+-----+
+|chrom|start|end|other2|mean1|mean2|mean3|
++-----+-----+---+------+-----+-----+-----+
+
+
+</help>
+</tool>