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+++ b/kmersvm/tomtom.xml	Sun Jun 16 18:06:14 2013 -0400
@@ -0,0 +1,84 @@
+<tool id="tomtom" name="Tomtom" version="1.0.0">
+
+	<description>Tomtom tool for motif searching</description>
+	<command>/home/galaxy/meme/bin/tomtom -no-ssc -internal -text -verbosity 1 -thresh $thresh 
+		#if str($cut.cut_choice) == 'e.value':
+			-evalue
+		#end if
+
+		#if str($dist.dist) == 'ed':
+			-dist ed
+		#elif str($dist.dist) == 'sw':
+			-dist sandelin
+		#else
+			-dist pearson	
+		#end if
+	
+	 $input1 /home/galaxy/meme/db/combined_db.meme > tomtom_out.txt
+	 
+	 </command>
+	 <inputs>
+	 	<param format="txt" name="input1" type="data" label="PWM File"/>
+		<param type="float" value="0.5" label="Threshold" name="thresh"/>
+	 	<conditional name="cut">
+	 		<param name="cut_choice" type="select" label="Threshold Type">
+	 			<option value="q.value" selected="true">q-value</option>
+	 			<option value="e.value">E-value</option>
+	 		</param>	
+	 	</conditional>
+	 	
+	 	<conditional name="dist">
+	 		<param name="dist" type="select" label="Distance Metric">
+	 			<option value="pearson" selected="true">Pearson</option>
+	 			<option value="ed">Euclidean</option>
+	 			<option value="sw">Sandelin-Wasserman Function</option>
+	 		</param>
+	 	</conditional>
+	 </inputs>
+	 
+	 <outputs>
+	 	<data format="txt" name="Tomtom Results" from_work_dir="tomtom_out.txt" label="${tool.name} on ${on_string}: Tomtom Matches"/>
+
+	 </outputs>
+	<help>
+
+Tomtom is a tool for comparing a DNA motif to a database of known motifs.  For an in-depth explanation of the Tomtom software see here_.
+
+----
+
+**Recommended Settings**
+
+We recommend most users use the Tomtom defaults of q-value for score, the cutoff of 0.5 and the Pearson correlation coefficent for distance metric.
+
+----
+
+**Parameters**
+
+We offer users the options of choosing which distance metric can be used to find matching motifs. Specifically, we offer the Pearson correlation coefficient, the Euclidean distance and the Sandelin-Wasserman Function.
+
+  * The Pearson correlation coefficient measures the similarity between columns of position weight matrices (PWMs).
+
+  * The Euclidean distance can be thought of as the length of the straight line between two PWMs.
+
+  * The Sandelin-Wasserman function sums the column-wise differences between PWMs.
+
+We also offer the choice of E-value and q-value to threshold the results returned by Tomtom.
+
+  * The E-value controls the expected number of false positives and can be any number.  
+
+  * The q-value controls the false discovery rate and is a number between 0 and 1.
+
+----
+
+Note that at this time we only offer Tomtom output in txt format.
+
+----
+
+**Citation**
+
+If you use this tool, please cite: Shobhit Gupta, JA Stamatoyannopolous, Timothy Bailey and William Stafford Noble, "Quantifying similarity between motifs", Genome Biology, 8(2):R24, 2007.
+
+.. _here: http://meme.nbcr.net/meme/tomtom-intro.html
+
+  </help>
+</tool>