--- a/dreme.xml	Sat Mar 10 08:17:36 2012 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,50 +0,0 @@
-<tool id="dreme" name="DREME">
-  <description>short motif discovery</description>
-  <command interpreter="python">/Users/xuebing/bin/dreme.py -p $input -png     -e $ethresh
-    #if $background_select.bg_select == "fromfile":
-        -n "${bgfile}"
-    #end if
-
-  &amp;&amp; mv dreme_out/dreme.html ${html_outfile}
-  
-  &amp;&amp; mv dreme_out/dreme.txt ${txt_outfile}
-
-  &amp;&amp; mv dreme_out/dreme.xml ${xml_outfile}
-  
-  &amp;&amp; rm -rf dreme_out
-  
-  </command>
-  <inputs>
-      <param name="input" type="data" format="fasta" label="Sequence file (FASTA)"/>      
-     <conditional name="background_select">
-    	<param name="bg_select" type="select" label="Background sequence" >
-		<option value="shuffle" selected="true">shuffle the orignal sequence</option>
-		<option value="fromfile">load from file</option>
-	    </param>
-	    <when value="fromfile">
-		    <param name="bgfile" type="data" format="fasta" label="Background sequence file (FASTA)"/>
-	    </when>
-    </conditional>
-          
-      <param name="ethresh" size="10" type="float" value="0.05" label="E-value threshold"/>
-  </inputs>
-  <outputs>
-
-    <data format="xml" name="xml_outfile" label="${tool.name} on ${on_string} (xml)"/>
-    <data format="txt" name="txt_outfile" label="${tool.name} on ${on_string} (motif)"/>
-    <data format="html" name="html_outfile" label="${tool.name} on ${on_string} (html)"/>    
-  </outputs>
-  <help>
-
-**What it does**
-
-http://meme.sdsc.edu/meme/doc/dreme.html
-
-DREME (Discriminative Regular Expression Motif Elicitation) finds relatively short motifs (up to 8 bases) fast, and can perform discriminative motif discovery if given a negative set, consisting of sequences unlikely to contain a motif of interest that is however likely to be found in the main ("positive") sequence set. If you do not provide a negative set the program shuffles the positive set to provide a background (in the role of the negative set).
-
-The input to DREME is one or two sets of DNA sequences. The program uses a Fisher Exact Test to determine significance of each motif found in the postive set as compared with its representation in the negative set, using a significance threshold that may be set on the command line.
-
-DREME achieves its high speed by restricting its search to regular expressions based on the IUPAC alphabet representing bases and ambiguous characters, and by using a heuristic estimate of generalised motifs' statistical significance. 
-
-  </help>
-</tool>