<tool id ="pySelectMotifsFromGTF" name="pySelectMotifsFromGTF">
	<requirements>
        	<requirement type="package">pyCRAC</requirement>
    	</requirements>
	<command interpreter="python"> 
	/usr/local/bin/pySelectMotifsFromGTF.py
	--gtf $input
	-m $motif
	-o $out
	-l $length
	-z $zscore	
	</command>
	<version_command>/usr/local/bin/pySelectMotifsFromGTF.py --version</version_command>
	<inputs>
		<param format="gtf" name="input" type="data" label="Input File -f" help="pyMotif gtf output files" />
		<param format="txt" name="motif" type="text" size="200" value="KBCTTG" label="motif string" help="Enter motif (all uppercase) you want to extract from the pyMotif gtf output file">
			<validator type="empty_field" />
		</param>
		<param format="integer" type="integer" value="6" size="5" name="length" label="Length --length" help="Set a Kmer Length. Note that the length has to be at least as long as your k-mer sequence, otherwise the program will not run correctly" />
		<param format="float" type="float" value="0" size="5" name="zscore" label="Z Score --Z_score" help="Set a minimum Kmer Z_score" />
		<param name="label" type="text" format="txt" size="30" value="pySelectMotifsFromGTF" label="Enter output file label -o" />
	</inputs>

	<outputs>
		<data format="gtf" name="out" label="${label.value}_${motif.value}.gtf"/>
	</outputs>
	<help>


.. class:: infomark

**pySelectMotifsFromGTF**

pySelectMotifsFromGTF is part of the pyCRAC_ package. Extracts your favourite k-mer sequence from pyMotif GTF output files.
Note that you can include degenerate nucleotides in your motif string::

    N = A, G, C or T
    R = A or G = puRine
    Y = C or T = pYrimidine
    M = A or C = aroMatic
    S = G or C
    W = A or T
    K = G or T = Keto
    V = A, C or G = Not T (letter after)
    D = A, G or T = Not C
    H = A, C or T = Not G
    B = C, G or T = Not A

So if you enter KBCTTG as search string and length=6, then the program will extract a large number of six-mers from your data.
If you set length = 8, it will look for this pattern in a stretch of 8 nucleotides.
   
.. _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 FILE, --output=FILE
                        Optional.Specify the name of the output file. Default
                        is standard output. Make sure it has the .gtf
                        extension!
    -m KBCTTG, --motif=KBCTTG
                        Specify the motif you want extract from the GTF file.
    -z 15.0, --Z_score=15.0
                        Set a minimum k-mer Z-score. Default=0
    -l 4, --length=4      
                        Set a k-mer length. Default is no length filtering

	</help>
</tool>