--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/fimo2-old.xml	Sat Mar 10 07:59:27 2012 -0500
@@ -0,0 +1,63 @@
+<tool id="fimo" name="motif search">
+  <description>using FIMO</description>
+  <command> fimo 
+    #if $background_select.bg_select == "fromfile":
+    -bgfile $bgfile
+    #end if
+    
+  $norc --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>
+    <conditional name="motif_selection">   
+        <param name="motif_sel" type="select" label="Motif Source">
+            <option value="user" selected="true">Use motif file in Your History</option>
+            <option value="known" >Known motif</option>
+        </param>
+        ##<when value="known">
+        ##    <param name="motif" type="select" label="Select motif">
+        ##        <option value="/Users/xuebing/galaxy-dist/tool-data/motif-database/5primerSpliceSite" selected="true">mouse 5 primer splice site</option>
+        ##        <option value="/Users/xuebing/galaxy-dist/tool-data/motif-database/5primerSpliceSite">mouse 3 primer splice site</option>
+        ##        <option value="/Users/xuebing/galaxy-dist/tool-data/motif-database/TATA-Box.meme">TATA box</option>
+        ##    </param>
+        ##</when>
+        <when value="user">
+            <param name="motif" type="data" format="txt" label="Motif file" help="created using the tool create-motif-file, or import from Shared Data"/>
+        </when>
+    </conditional>     
+         
+    <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="0.01" 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>