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