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author xuebing
date Sat, 31 Mar 2012 21:41:37 -0400
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files iupac_to_meme.xml
diffstat 1 files changed, 59 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/iupac_to_meme.xml	Sat Mar 31 21:41:37 2012 -0400
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+<tool id="iupac_to_meme" name="create_MEME_motif_file">
+  <description>from one sequence</description>
+  <command>iupac2meme 
+    #if $background_select.bg_select == "fromfile":
+    -bg $bgfile
+    #end if
+  -numseqs $numseqs $logodds $motif > $output </command>
+  <inputs>
+      <param name="motif" size="20" type="text" value="AATAAA" label="motif sequence" help="IUPAC motif, such as ACGGWNYCGT"/>
+      <conditional name="background_select">
+    	<param name="bg_select" type="select" label="Background model" >
+		  <option value="uniform" selected="true">uniform</option>
+		  <option value="fromfile">load from file</option>
+	    </param>
+	    <when value="fromfile">
+		    <param name="bgfile" type="data" format="txt" label="File for background model"/>
+	    </when>
+    </conditional>
+    
+      <param name="numseqs" size="10" type="integer" value="20" label="Number of sequences (-numseqs)" help="assume frequencies based on this many sequences; default: 20"/>
+    <param name="logodds" label="also output log-odds (PSSM)" help="output the log-odds (PSSM) and frequency (PSPM) motifs; default: PSPM motif only" type="boolean" truevalue="-logodds" falsevalue="" checked="False"/>
+  </inputs>
+  <outputs>
+    <data format="txt" name="output" label="$motif-meme"/>
+  </outputs>
+  <help>
+
+**Description**
+
+Convert an IUPAC motif into a MEME version 4 formatted file suitable for use with FIMO and other MEME Suite programs.
+
+See additional information: 
+
+http://meme.sdsc.edu/meme/doc/iupac2meme.html
+
+**IUPAC code**::
+
+    Nucleotide Code:  Base:
+    ----------------  -----
+    A.................Adenine
+    C.................Cytosine
+    G.................Guanine
+    T (or U)..........Thymine (or Uracil)
+    R.................A or G
+    Y.................C or T
+    S.................G or C
+    W.................A or T
+    K.................G or T
+    M.................A or C
+    B.................C or G or T
+    D.................A or G or T
+    H.................A or C or T
+    V.................A or C or G
+    N.................any base
+
+
+
+  </help>
+</tool>