<tool id="pyGTF2bed" name="pyGTF2bed">
	  <description>converter</description>
	  <requirements>
        	<requirement type="package">pyCRAC</requirement>
    	  </requirements>
 	  <command interpreter="python">/usr/local/bin/pyGTF2bed.py --gtf $input -o $output
	  #if $addtrack.track == "--track":
	   --track
	   --name $addtrack.name
	   --description $addtrack.description
	   #if $addtrack.colorscheme.colorsel == "default":
	    -c $addtrack.colorscheme.color
	   #else:
	    -s '$addtrack.colorscheme.plus,$addtrack.colorscheme.minus'
	   #end if#
	  #end if#
 	  </command>
	  <version_command>/usr/local/bin/pyGTF2bed.py --version</version_command>
 	  <inputs>
	      <param name="input" type="data" format="gtf" label="GTF file --gtf"/>
	      <conditional name="addtrack">
		<param name="track" type="select" label="Add UCSC track line to output --track">
		  <option value="" selected="true">NO</option>
		  <option value="--track">YES</option>
		</param>
		<when value=""/>
		<when value="--track">
		  <param name="name" format="txt" type="text" value="User_supplied_track" size="80" label="Track name -n"/>
                  <param name="description" format="txt" type="text" value="User_supplied_track" size="80" label="Track description -d"/>
		  <conditional name="colorscheme">
		  <param name="colorsel" type="select" label="Colouring scheme">
		    <option value="default" selected="true">One Colour</option>
		    <option value="strand">By Strand</option>
		  </param>
		  <when value="default">
		    <param name="color" type="select" label="Choose track colour -c">
		      <option value="black" selected="true">Black</option>
		      <option value="red">Red</option>
                      <option value="blue">Blue</option>
                      <option value="green">Green</option>
                      <option value="purple">Purple</option>
		    </param>            
		  </when>
                  <when value="strand">
                    <param name="plus" type="select" label="Choose forward strand track colour -s">
                      <option value="black" selected="true">Black</option>
                      <option value="red">Red</option>
                      <option value="blue">Blue</option>
                      <option value="green">Green</option>
                      <option value="purple">Purple</option>
                    </param>
		    <param name="minus" type="select" label="Choose minus strand track colour -s">
                      <option value="black" selected="true">Black</option>
                      <option value="red">Red</option>
                      <option value="blue">Blue</option>
                      <option value="green">Green</option>
                      <option value="purple">Purple</option>
		    </param>
                  </when>
		  </conditional>
		</when>
	      </conditional>
	      <param name="label" type="text" format="txt" size="30" value="pyGTF2bed" label="Enter output file label -o" />
 	  </inputs>
 	  <outputs>
	    <data name="output" format="bed6" label="${label.value}.bed"/>
 	  </outputs>
	  <help>

.. class:: infomark

**pyGTF2bed**

pyGTF2bed is part of the pyCRAC_ package. Converts GTF files to the bed 6 format. Gene names present in the GTF file will be included in the bed file.

   
.. _pyCRAC: http://sandergranneman.bio.ed.ac.uk/Granneman_Lab/pyCRAC_software.html
        
------

**Parameter list**

These options can be used to add and modify a track line for the UCSC genome browser::

    --track             
                        Use this flag to add a UCSC genome browser track line
                        to the beginning of your file
    -n NAME, --name=NAME
                        For the USCS track line: provide a track name. Default
                        = 'User_supplied_track'
    -d DESCRIPTION, --description=DESCRIPTION
                        For the USCS track line: provide a track description.
                        Default = 'User_supplied_track'
    -c COLOR, --color=COLOR
                        select the track color. Default = black
    -s STRANDS, --colorstrands=STRANDS
                        select the colors for each strand. Default =
                        'red,blue'

File input options::

    --gtf=Yourfavoritegtf.gtf
                        type the path to the gtf file that you want to
                        convert. Default is standard input
 	  </help>
</tool>