--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/carpet-src-1/tools/CARPET/genecentrico.xml	Tue Jun 07 16:50:41 2011 -0400
@@ -0,0 +1,75 @@
+<tool id="BECorrelation" name="BEC" version="1.0.0">
+  <description>Binding-Expression-Correlation</description>
+  <command interpreter="perl">genecentrico.pl $expr $chip_gff ${prom_choice.prom_start} ${prom_choice.type} $result $output ${prom_choice.prom_end}</command>
+  <inputs>
+    <param format="tabular" name="expr" type="data" label="expression file"/>
+    <param format="bed" name="chip_gff" type="data" label="ChIP on chip GFF results"/>
+    <conditional name="prom_choice">
+   		<param name="type" type="select" label="Analysis type">
+    	  <option value="promoter">only promoter</option>
+    	  <option value="all">all gene</option>
+   	    </param>
+   	    <when value="promoter">
+   	    		<param name="prom_start" type="integer" size="10" value="-2000" label="Promoter start"/>
+   				<param name="prom_end" type="integer" size="10" value="1000" label="Promoter end"/>
+   		</when>
+   		<when value="all">
+   				<param name="prom_start" type="integer" size="10" value="-2000" label="Promoter start"/>
+   				<param name="prom_end" type="text" size="12" value="NOT-NEEDED" label="Promoter end"/>
+   		</when>		
+   </conditional>
+   <param name="result" type="select" label="result output">
+      <option value="number"># of matches</option>
+      <option value="max_value">max value</option>
+     </param> 
+  </inputs>
+  <outputs>
+    <data format="tabular" name="output" />
+  </outputs>
+	<help>
+ .. class:: infomark
+
+**What it does**
+
+BEC integrates the results of expression analysis and ChIP-chip analysis. For each transcript the number of peaks matching in the promoter and/or within the gene body is calculated.
+
+PLEASE, for more detailed information refer to the CARPET user Manual:
+click to download_ it.
+
+.. _download: /static/example_file/CARPET_userManual.zip
+
+-----
+
+**Parameters:**
+
+- **Analysis type:** 
+                     - **promoter:** only the peaks matching in the promoter region (defined by user) are associated with the transcript
+                     - **all gene:** peaks matching in the promoter and within the gene body are associated with the transcript
+- **result output:** 
+	- **# of matches:** the number of matching peaks are reported
+	- **max value:** the highest score among all matching peaks is reported
+                     
+--------
+
+.. class:: warningmark
+
+If a peak matches with more than one transcript, it is associated with both.
+
+-----
+
+**INPUT FILES**
+
+- Expression file: file created by TEA
+- ChIP on chip GFF results: file create by PeakPicker (or any GFF file)
+
+**OUTPUT FILES**
+
+.. image:: static/images/CARPET/bec_output.png
+
+.. class:: infomark
+
+This results table can be used again as input expression file, to add another ChIP-chip experiment.
+
+	</help>
+
+</tool>