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