--- a/iupac2meme.xml	Sat Mar 10 08:17:36 2012 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,59 +0,0 @@
-<tool id="iupac2meme" name="create-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>