view fastaptamer_search_1.xml @ 0:8603505f43c5 draft

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<tool id="fastaptamer_search_1_0_2" name="FASTAptamer-Search" version="1.0.2">

	<description>Degenerate motif searching</description>
	
	<version_command>fastaptamer_search -v</version_command>
	
	<command interpreter="perl">fastaptamer_search -i $input -o $output -p $pattern
	</command>
	
	<inputs>
		<param name="input" type="data" format="fasta" label="Input file" ></param>
		<param name="pattern" type="text" label="Pattern to search for"></param>
 	</inputs>
 	
    <outputs>
    	<data name="output" format="fasta" label="FASTAptamer-Search output file"></data>
 	</outputs>
	
 	<help>


**FASTAptamer-Search** searches for degenerate nucleotide motifs within a sequence file. 

Patterns and input sequence data are case insensitive, and T/U are interchangeable. In addition to single bases, patterns can include any of the degenerate base symbols from IUPAC-IUBMB nucleic acid notation: ::

	A/T/G/C/U	single bases
	R		puRines (A/G)
	Y		pYrimidines (C/T)
	W		Weak (A/T)
	S		Strong (G/C)
	M		aMino (A/C)
	K		Keto (G/T)
	B		not A
	D		not C
	H		not G
	V		not T
	N		aNy base (not a gap)


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.. image:: 
	http://burkelab.missouri.edu/images/fastaptamer-logo-xs.png
	:height: 98
	:width: 300

For more information on FASTAptamer, visit our website_.

FASTAptamer is distributed under a GNU GPL v3.0 license. For complete license click here_.

.. _here: http://burkelab.missouri.edu/fastaptamer/LICENSE.txt
.. _website: http://burkelab.missouri.edu/fastaptamer.html

    </help>

	<citations>
    	<citation type="doi">doi:10.1038/mtna.2015.4</citation>
    </citations>
	
</tool>