<tool id ="pyGetGTFSources" name="pyGetGTFSources">
	<requirements>
        	<requirement type="package">pyCRAC</requirement>
    	</requirements>
	<command interpreter="python"> 
	/usr/local/bin/pyGetGTFSources.py --gtf $addGTF.gtf --count -o $out
	</command>
	<version_command>/usr/local/bin/pyGetGTFSources.py --version</version_command>
	<inputs>
		<conditional name="addGTF">
			<param name="gtfFile" type="select"  label="Choose GTF File from">
				<option value="default" selected="true">Defaults</option>
				<option value="other">History</option>
			</param>	
			<when value="default">
				<param name="gtf" type="select"  label="GTF File --gtf" help="GTF file containing gene ID co-ordinates">
					<options from_data_table="pycrac_gtf"/>
				</param>
			</when>
			<when value="other">
				<param format="GTF" name="gtf" type="data" label="GTF File --gtf" help="GTF file containing gene ID co-ordinates"/>
			</when>
		</conditional>
		<param name="count" type="select"  label="Count occurences of each annotation --count">
                                <option value="" selected="true">No</option>
                                <option value="--count">Yes</option>
		</param>
                <param name="label" type="text" format="txt" size="30" value="GTF sources list" label="Enter output file label -o" />
	</inputs>

	<outputs>
		<data format="tabular" name="out" label="${label.value}.txt"/>
	</outputs>
	<help>
.. class:: infomark

**pyGetGTFSources**

pyGetGTFSources is part of the pyCRAC_ package. Extracts source names from the second column in a GTF file.


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

**Parameter list**

Options::

  --gtf=Yourfavoritegtf.gtf
                        type the path to the gtf file that you want to use. By
                        default it expects data from the standard input
  -o OUTFILE, --outfile=OUTFILE
                        type the name and path of the file you want to write
                        the output to. Default is standard output
  --count               with this flag you the program will count the
                        occurence for each source/annotation in the gtf file




	</help>
</tool>