--- a/bwBinavg.xml	Sat Mar 10 08:17:36 2012 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,44 +0,0 @@
-<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>