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<tool id="removeRow" name="Remove CLIP tags with deletions">
  <description></description>
  
  <command interpreter="perl">
	/home/galaxy/tools/CTK/removeRow.pl -q $QueryColumnID -f $FilterColumnID $IgnoreCase $ReverseMode  $input1 $input2  &gt; $output
  </command>

  <inputs>
	<param type="data" format="bed" name="input1" label="Input file in BED format of unique CLIP tags"/>
	<param type="data" format="bed" name="input2" label="Input file in BED format of CIMS" />
    
	<param name="QueryColumnID" type="integer" value="3" label="Query column id (zero-based)"/>
	<param name="FilterColumnID" type="integer" value="3" label="Filter column id (zero-based)"/>
       
	<param name="IgnoreCase" type="boolean" truevalue="-i" falsevalue="" checked="no" label="Ignore case" />
	<param name="ReverseMode" type="boolean" truevalue="-r" falsevalue="" checked="no" label="Reverse mode" />
  </inputs>
  
  <outputs>
	<data name="output" format="bed" />
  </outputs>
  <help>

.. class:: infomark

**What this tool does**

Since the vast majority of deletions are introduced because of cross linking, tags with deletions are treated as read-through tags and removed. 

This tool will remove selected rows from a file. Here it will output file in BED format in which CLIP tags with deletions are removed.

Note: The parameters 3 and 3 indicate the columns in the two input files.
  </help>
</tool>