<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>