Mercurial > repos > fastaptamer > fastaptamer_search
comparison fastaptamer_search_1.xml @ 0:8603505f43c5 draft
Uploaded
| author | fastaptamer |
|---|---|
| date | Tue, 10 Feb 2015 14:50:45 -0500 |
| parents | |
| children |
comparison
equal
deleted
inserted
replaced
| -1:000000000000 | 0:8603505f43c5 |
|---|---|
| 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> |