--- a/fimo2.xml	Sat Mar 10 08:17:36 2012 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,47 +0,0 @@
-<tool id="fimo" name="motif search">
-  <description>using FIMO</description>
-  <command> fimo 
-    #if $background_select.bg_select == "fromfile":
-    -bgfile $bgfile
-    #end if
-    
-  $norc --max-stored-scores 5000000 --output-pthresh $pth --verbosity 1 $motif $database 
-  &amp;&amp; mv fimo_out/fimo.html ${html_outfile}
-  
-  &amp;&amp; mv fimo_out/fimo.txt ${txt_outfile}
-  
-  &amp;&amp; rm -rf fimo_out
-  
-  </command>
-  <inputs>
-    
-            <param name="motif" type="data" format="txt" label="Motif file" help="created using the tool create-motif-file, or import from Shared Data"/>         
-    <param name="database" type="data" format="fasta" label="Sequence file (FASTA)"/>
-      
-    <conditional name="background_select">
-    	<param name="bg_select" type="select" label="Background model" >
-		  <option value="uniform" selected="true">uniform</option>
-		  <option value="fromfile">load from file</option>
-	    </param>
-	    <when value="fromfile">
-		    <param name="bgfile" type="data" format="txt" label="File for background model"/>
-	    </when>
-    </conditional>
-      
-      <param name="pth" size="10" type="float" value="0.0001" label="p-value threshold"/>
-    <param name="norc" label="Do not score the reverse complement DNA strand. Both strands are scored by default" type="boolean" truevalue="-norc" falsevalue="" checked="False"/>
-  </inputs>
-  <outputs>
-    <data format="html" name="html_outfile" label="${tool.name} on ${on_string} (html)"/>
-    <data format="txt" name="txt_outfile" label="${tool.name} on ${on_string} (txt)"/>
-  </outputs>
-  <help>
-
-**What it does**
-
-This tool uses FIMO to find matches of a motif in a fasta file. See more details:
-
-http://meme.sdsc.edu/meme/fimo-intro.html
- 
-  </help>
-</tool>