--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mytools/phastCons.xml	Tue Mar 13 23:34:52 2012 -0400
@@ -0,0 +1,48 @@
+<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>