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comparison mytools/iupac2meme.xml @ 0:39217fa39ff2

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author xuebing
date Tue, 13 Mar 2012 23:34:52 -0400
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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>