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

    <description>TYPE_DESCRIPTION_HERE</description>

    <command interpreter="bash">
	names=""
	inputfiles=""
	#for $i, $s in enumerate($annotateColumn)
		names=$names + ${s.colname} + " "
		inputfiles=$inputfiles+ ${s.colfile} + " "
	#end for
	bedtools annotate $countflag -names $names -i $inputRegion -files $inputfiles
	</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" />
  
    </outputs>

<help>

.. class:: infomark

IMPORTANT INFORMATION

----

WRITE HELP HERE

</help>

</tool>