view annotateBedWrapper.xml @ 5:39fa27e915bf draft

Uploaded
author xiaoyi-cao
date Sun, 02 Dec 2012 14:47:12 -0500
parents d022f9da02c7
children 133b692c999c
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<tool id="annotateBed" name="annotateBed">

    <description>Annotate BED files with overlapping BED files</description>

    <command>
	bedtools annotate 
	$countflag
	-i '$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>