--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/methylation_analysis_bismark/methylation_analysis/methylation_by_region_converter.xml	Tue Dec 04 20:15:26 2012 -0500
@@ -0,0 +1,69 @@
+<tool id="methyation_by_region_tool" name="Methylation by Region Converter" version="0.1.1">
+  <description>: create a bedgrapgh with methylation percentages aggregated by region</description>
+  <requirements>
+    <requirement type="package" version="0.1.16">samtools</requirement>
+    <requirement type="package" version="0.12.7">bowtie2</requirement>
+  </requirements>
+  <command interpreter="perl">
+    
+	methylation_by_region_converter.pl
+	
+	-o $output
+	-l $summary
+	## Handle reference file.
+        #if $refBedSource.bedSource == "history":
+            $refBedSource.ownFile
+        #else:
+            "${refBedSource.index.fields.path}"
+        #end if
+	$bedgraph
+
+  </command>
+	<inputs>
+		<conditional name="refBedSource">
+		  <param name="bedSource" type="select" label="Will you select a bed file from your history or use a built-in one?" help="Built-ins were created using default options">
+		    <option value="indexed">Use a built-in index</option>
+		    <option value="history">Use one from the history</option>
+		  </param>
+		  <when value="indexed">
+		    <param name="index" type="select" label="Select a bed file" help="If bed file is not listed, contact the Galaxy team">
+		      <options from_data_table="bismark_bed_files">
+		        <filter type="sort_by" column="1"/>
+		        <validator type="no_options" message="No files are available for the selected input dataset"/>
+		      </options>
+		    </param>
+		  </when>
+		  <when value="history">
+		    <param name="ownFile" type="data" format="bed" metadata_name="dbkey" label="Select the bed file" />
+		  </when>  <!-- history -->
+		</conditional>  <!-- refGenomeSource -->
+		<param name="bedgraph" type="data" format="bedgraph" label="BedGraph file" />
+		<param name="sample" type="text" label="Sample Name" />
+	
+	</inputs>
+	<outputs>
+		<data name="output" format="tabular" label="${tool.name} on ${on_string}" />
+		<data name="summary" format="txt" label="${tool.name} summary" />
+	</outputs>
+	<help>
+|
+
+
+**What it does**
+
+
+Script to take a bed file of target regions and a series of bedgraphs from bismark and create a bedgrapgh with methylation percentages aggregated by region
+
+
+-----
+ 
+
+::
+
+  Usage:   methylation_by_region_converter.pl [OPTIONS] bed_file bedGraph
+
+
+	</help>
+</tool>
+
+