# HG changeset patch
# User fastaptamer
# Date 1421280511 18000
# Node ID 119f3b536f609e2693e9198f22cced9bf8f0f042
# Parent  7a29d36b8f8557b58e671ba219d55d9097076561
Uploaded

diff -r 7a29d36b8f85 -r 119f3b536f60 fastaptamer_search_1.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/fastaptamer_search_1.xml	Wed Jan 14 19:08:31 2015 -0500
@@ -0,0 +1,60 @@
+<tool id="fastaptamer_search_1_0_1" name="FASTAptamer-Search" version="1.0.1">
+
+	<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)
+
+
+------
+
+.. 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.2015.7X</citation>
+    </citations>
+	
+</tool>