<tool id="bedExt" name="Get the position before the start site">
  <description>as a potential cross link site that causes truncation</description>
  <command interpreter="perl">
	/home/galaxy/tools/CTK/bedExt.pl -n $NeighborRegion -l $LeftExtension -r $RightExtension -v $input $output
  </command>

  <inputs>
        <param name="input" type="data" format="bed" label="Input BED file in which CLIP tags with deletions were removed"/>
        <param name="NeighborRegion" type="text" value="up" label="Get neighbor region relative to up|down|r=100"/>
        <param name="LeftExtension" type="integer" value="-1" label="Extension on the left, with sign 0"/>
        <param name="RightExtension" type="integer" value="-1" label="Extension on the right, with sign 0"/>
  </inputs>
  
  <outputs>
        <data name="output" format="bed" label="Output file in BED format extended around start site as a potential cross link site that causes truncation" />
  </outputs>
  <help>

.. class:: infomark

**What this tool does**

This tool will extract sequences specied by a bed file. 

Here it  will take as input files in BED format in which CLIP tags with deletions were removed and output files in BED format extended around start site as a potential cross link site that causes truncation.
  </help>
</tool>