--- a/phastCons.xml	Sat Mar 10 08:17:36 2012 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,48 +0,0 @@
-<tool id="getScore" name="conservation">
-  <description>phastCons or phyloP,vertebrate30way</description>
-  <command interpreter="python">getGenomicScore.py $input $output $score_type $score_path $nbin $strand $outplot $span</command>
-  <inputs>
-      <param name="input" format="interval" type="data" label="Interval file"/>
-      <param name="score_path" type="select" label="Select score" >
-      <option value="/Users/xuebing/galaxy-dist/tool-data/genome/mm8/phastcons" >mm8-phastCons17way</option>
-		  <option value="/Users/xuebing/galaxy-dist/tool-data/genome/mm9/phastcon" selected="true">mm9-phastCons30way-vertebrate</option>
-          <option value="/Users/xuebing/galaxy-dist/tool-data/genome/mm9/phyloP30way">mm9-phyloP30way-vertebrate</option>
-          <option value="/Users/xuebing/galaxy-dist/tool-data/genome/hg18/phastCons28wayPlacMam">hg18-phastCons28wayPlacMam</option>                      </param>
-      <param name="score_type" type="select" label="Select score summary type" >
-		  <option value="mean" selected="true">mean</option>
-		  <option value="max">maximum</option>
-		  <option value="min">minimum</option>
-		  <option value="std">standard deviation</option>
-		  <option value="coverage">coverage:fraction covered</option>
-      </param>
-      <param name="nbin" type="integer" value="1" label="number of bins"/> 
-       <param name="span" size="10" type="float" value="0.1" label="loess span: smoothing parameter" help="value less then 0.1 disables smoothing"/>         
-      <param name="strand" type="integer" value="0" label="Specify the strand column" help="leave 0 to ignore strand information. Only matters if using more than 1 bin"/>          
-  </inputs>
-  <outputs>
-     <data format="pdf" name="outplot" label="${tool.name} on ${on_string}[plot]"/>
-    <data format="interval" name="output" label="${tool.name} on ${on_string}[data]"/>
-  </outputs>
-  <help>
-
-.. class:: infomark
-
-The score for each interval is added as a new column 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 return the mean of phastCons scores, your output will look like this:
-
-+-----+-----+---+------+----+
-|chrom|start|end|other2|mean|
-+-----+-----+---+------+----+
-
-
-</help>
-</tool>