<tool id ="pyGetGeneNamesFromGTF" name="pyGetGeneNamesFromGTF">
	<requirements>
        	<requirement type="package">pyCRAC</requirement>
    	</requirements>
	<command interpreter="python"> 
	/usr/local/bin/pyGetGeneNamesFromGTF.py --gtf $addGTF.gtf --attribute $attribute $count -o $out
	</command>
	<version_command>/usr/local/bin/pyGetGeneNamesFromGTF.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="attribute" type="select"  label="Select the attribute to extract names from --attribute">
                                <option value="gene_name" selected="true">gene_name</option>
                                <option value="gene_id">gene_id</option>
                                <option value="transcript_name">transcript_name</option>
                                <option value="transcript_id">transcript_id</option>
		</param>
                <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 gene list" label="Enter output file label -o" />
	</inputs>

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

**pyGetGeneNamesFromGTF**

pyGetGeneNamesFromGTF is part of the pyCRAC_ package. Extracts and counts all gene names from 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
  -a ATTRIBUTE, --attribute=ATTRIBUTE
                        from which attribute do you want to extract names?
                        Choices: gene_name, gene_id, transcript_name,
                        transcript_id
  --count               
                        with this flag you the program will count the
                        occurence for each source/annotation in the gtf file


	</help>
</tool>