<tool id="pyCalculateChromosomeLengths" name="pyCalculateChromosomeLengths">
	  <requirements>
        	<requirement type="package">pyCRAC</requirement>
    	  </requirements>
 	  <command interpreter="python">
	  /usr/local/bin/pyCalculateChromosomeLengths.py 
	  -f $ftype.input 
	  --file_type $ftype.filetype 
	  -o $output </command>
	  <version_command>/usr/local/bin/pyCalculateChromosomeLengths.py --version</version_command>
 	  <inputs>
	      <conditional name="ftype">
	      <param name="filetype" type="select"  label="File type">
                                        <option value="fasta" selected="true">Fasta</option>
                                        <option value="tab">Tab</option>
	      </param>        
	      <when value="fasta">
		              <param name="input" type="data" format="fasta" label="Input file" help="Fasta or Tab file"/>
	      </when>
	      <when value="tab">
                              <param name="input" type="data" format="tabular" label="Input file" help="Fasta or Tab file"/>
	      </when>
	      </conditional>
 	  </inputs>
	  <param name="label" type="text" format="txt" size="30" value="pyCalculateChromosomeLengths" label="Enter output file label -o" />
 	  <outputs>
	    <data name="output" format="txt" label="${label.value}.len"/>
 	  </outputs>
	  <help>

.. class:: infomark

**pyCalculateChromosomeLengths**

pyCalculateChromosomeLengths is part of the pyCRAC_ package. Takes a genome sequence in fasta or tab format and generates a tab-delimited file showing chromosome name and chromosome length.
   
.. _pyCRAC: http://sandergranneman.bio.ed.ac.uk/Granneman_Lab/pyCRAC_software.html

-------

**Parameter list**                                                                     

Options::

  -f chromosomes.fasta, --input_file=chromosomes.fasta
                        provide the name and path of your fasta or tab genomic
                        sequence file. Default is standard input.
  --file_type=fasta     
                        provide the file type (fasta or tab). Default is fasta

 	  </help>
</tool>