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

	<description> the depth &amp; breadth of coverage of features from multiple 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 format="bed" name="inputRegion" type="data" label="The regions to be annotated is in this file:" />
        <param name="countflag" type="select" label="What to report in the output: ">
			<option value="-counts" selected="true">the count of features in each file that overlap the regions</option>
			<option value="">fraction of the region covered by each feature</option>
			<option value="-both">Report the counts followed by the % coverage</option>
		</param>
		<repeat name="annotateColumn" title="Column">
			<param name="colname" type="text" label="Feature name" />
			<param name="colfile" type="data" format="bed" label="Feature file to annotate for the column" />
		</repeat>

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

<help>

**What it does**

This tool is used to annotate the regions in a bed file with features provided in multiple BED files.

..class:: warningmark

This tool requires that bedtools__ has been installed on your system.

-----

</help>

</tool>