0
+ − 1 <tool id="fastaptamer_search_1_0_2" name="FASTAptamer-Search" version="1.0.2">
+ − 2
+ − 3 <description>Degenerate motif searching</description>
+ − 4
+ − 5 <version_command>fastaptamer_search -v</version_command>
+ − 6
+ − 7 <command interpreter="perl">fastaptamer_search -i $input -o $output -p $pattern
+ − 8 </command>
+ − 9
+ − 10 <inputs>
+ − 11 <param name="input" type="data" format="fasta" label="Input file" ></param>
+ − 12 <param name="pattern" type="text" label="Pattern to search for"></param>
+ − 13 </inputs>
+ − 14
+ − 15 <outputs>
+ − 16 <data name="output" format="fasta" label="FASTAptamer-Search output file"></data>
+ − 17 </outputs>
+ − 18
+ − 19 <help>
+ − 20
+ − 21
+ − 22 **FASTAptamer-Search** searches for degenerate nucleotide motifs within a sequence file.
+ − 23
+ − 24 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: ::
+ − 25
+ − 26 A/T/G/C/U single bases
+ − 27 R puRines (A/G)
+ − 28 Y pYrimidines (C/T)
+ − 29 W Weak (A/T)
+ − 30 S Strong (G/C)
+ − 31 M aMino (A/C)
+ − 32 K Keto (G/T)
+ − 33 B not A
+ − 34 D not C
+ − 35 H not G
+ − 36 V not T
+ − 37 N aNy base (not a gap)
+ − 38
+ − 39
+ − 40 ------
+ − 41
+ − 42 .. image::
+ − 43 http://burkelab.missouri.edu/images/fastaptamer-logo-xs.png
+ − 44 :height: 98
+ − 45 :width: 300
+ − 46
+ − 47 For more information on FASTAptamer, visit our website_.
+ − 48
+ − 49 FASTAptamer is distributed under a GNU GPL v3.0 license. For complete license click here_.
+ − 50
+ − 51 .. _here: http://burkelab.missouri.edu/fastaptamer/LICENSE.txt
+ − 52 .. _website: http://burkelab.missouri.edu/fastaptamer.html
+ − 53
+ − 54 </help>
+ − 55
+ − 56 <citations>
+ − 57 <citation type="doi">doi:10.1038/mtna.2015.4</citation>
+ − 58 </citations>
+ − 59
+ − 60 </tool>
