Mercurial > repos > xuebing > sharplabtool
comparison iupac2meme.xml @ 14:76e1b1b21cce default tip
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| author | xuebing |
|---|---|
| date | Tue, 13 Mar 2012 19:05:10 -0400 |
| parents | 292186c14b08 |
| children |
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| 13:292186c14b08 | 14:76e1b1b21cce |
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| 1 <tool id="iupac2meme" name="create-motif-file"> | |
| 2 <description>from one sequence</description> | |
| 3 <command>iupac2meme | |
| 4 #if $background_select.bg_select == "fromfile": | |
| 5 -bg $bgfile | |
| 6 #end if | |
| 7 -numseqs $numseqs $logodds $motif > $output </command> | |
| 8 <inputs> | |
| 9 <param name="motif" size="20" type="text" value="AATAAA" label="motif sequence" help="IUPAC motif, such as ACGGWNYCGT"/> | |
| 10 <conditional name="background_select"> | |
| 11 <param name="bg_select" type="select" label="Background model" > | |
| 12 <option value="uniform" selected="true">uniform</option> | |
| 13 <option value="fromfile">load from file</option> | |
| 14 </param> | |
| 15 <when value="fromfile"> | |
| 16 <param name="bgfile" type="data" format="txt" label="File for background model"/> | |
| 17 </when> | |
| 18 </conditional> | |
| 19 | |
| 20 <param name="numseqs" size="10" type="integer" value="20" label="Number of sequences (-numseqs)" help="assume frequencies based on this many sequences; default: 20"/> | |
| 21 <param name="logodds" label="also output log-odds (PSSM)" help="output the log-odds (PSSM) and frequency (PSPM) motifs; default: PSPM motif only" type="boolean" truevalue="-logodds" falsevalue="" checked="False"/> | |
| 22 </inputs> | |
| 23 <outputs> | |
| 24 <data format="txt" name="output" label="$motif-meme"/> | |
| 25 </outputs> | |
| 26 <help> | |
| 27 | |
| 28 **Description** | |
| 29 | |
| 30 Convert an IUPAC motif into a MEME version 4 formatted file suitable for use with FIMO and other MEME Suite programs. | |
| 31 | |
| 32 See additional information: | |
| 33 | |
| 34 http://meme.sdsc.edu/meme/doc/iupac2meme.html | |
| 35 | |
| 36 **IUPAC code**:: | |
| 37 | |
| 38 Nucleotide Code: Base: | |
| 39 ---------------- ----- | |
| 40 A.................Adenine | |
| 41 C.................Cytosine | |
| 42 G.................Guanine | |
| 43 T (or U)..........Thymine (or Uracil) | |
| 44 R.................A or G | |
| 45 Y.................C or T | |
| 46 S.................G or C | |
| 47 W.................A or T | |
| 48 K.................G or T | |
| 49 M.................A or C | |
| 50 B.................C or G or T | |
| 51 D.................A or G or T | |
| 52 H.................A or C or T | |
| 53 V.................A or C or G | |
| 54 N.................any base | |
| 55 | |
| 56 | |
| 57 | |
| 58 </help> | |
| 59 </tool> |