<tool id="annotateBed" name="annotateBed">

    <description>Annotate BED files with overlapping BED files</description>
	
	<requirements>
		<requirement type="binary">annotateBed</requirement>
		<requirement type="package">bedtools</requirement>
	</requirements>

    <command>
	annotateBed 
	$countflag
	-i '$inputRegion'
	-names 
	#for $i, $s in enumerate($annotateColumn)
		'${s.colname}'
	#end for
	-files
	#for $i, $s in enumerate($annotateColumn)
		'${s.colfile}'
	#end for
	&gt; '$output'
	</command>

    <inputs>

        <param name="countflag" type="boolean" label="Use count to annotate" truevalue="-count" falsevalue="" />
        <param format="bed" name="inputRegion" type="data" label="The region to be annotated" />
		<repeat name="annotateColumn" title="Column">
			<param name="colname" type="text" label="Column name" />
			<param name="colfile" type="data" format="bed" label="BED file to annotate for the column" />
		</repeat>

    </inputs>
    <outputs>
        <data format="bed" name="output" metadata_source="inputRegion" label="${inputRegion.name} annotated" />
    </outputs>

<help>

.. class:: infomark

IMPORTANT INFORMATION

----

WRITE HELP HERE

</help>

</tool>