--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mutation_analysis.xml	Fri Mar 18 07:50:34 2016 -0400
@@ -0,0 +1,54 @@
+<tool id="mutation_analysis_shm" name="Mutation Analysis" version="1.0">
+	<description></description>
+	<command interpreter="bash">
+		wrapper.sh $in_file $method $out_file $out_file.files_path ${in_file.name} ${include_fr1} $functionality $unique $naive_output $filter_uniques
+	</command>
+	<inputs>
+		<param name="in_file" type="data" label="IMGT zip file to be analysed" />
+		<param name="method" type="select" label="Identification method" help="" >
+			<option value="custom" selected="true">custom</option>
+			<option value="blastn">blastn</option>
+		</param>
+		<param name="include_fr1" type="select" label="Include mutations in FR1 region" help="" >
+			<option value="yes">yes</option>
+			<option value="no" selected="true">no</option>
+		</param>
+		<param name="functionality" type="select" label="Functionality filter" help="" >
+			<option value="productive" selected="true">Productive: Keep "productive" and "productive (see comment)"</option>
+			<option value="unproductive">Unproductive: Keep "unproductive" and "unproductive (see comment)"</option>
+			<option value="remove_unknown">Remove "unknown" and "unknown (see comment)"</option>
+			<option value="dont_filter">Don't filter</option>
+		</param>
+		
+		<param name="unique" type="select" label="Remove duplicates based on" help="" >
+			<option value="AA.JUNCTION_V_subclass" selected="true">AA.JUNCTION + V + subclass</option>
+			<option value="AA.JUNCTION_subclass">AA.JUNCTION + subclass</option>
+			<option value="AA.JUNCTION_V">AA.JUNCTION + V</option>
+			<option value="AA.JUNCTION">AA.JUNCTION</option>
+			<option value="none">Don't remove duplicates</option>
+		</param>
+		<conditional name="naive_output_cond">
+			<param name="naive_output" type="select" label="Output a file for naive analysis?">
+				<option value="yes">Yes</option>
+				<option value="no" selected="true">No</option>
+			</param>
+		</conditional>
+		<param name="filter_uniques" type="select" label="Filter unique sequences" help="Filter out the sequences (based on CDR1, FR2, CDR2, FR3 and CDR3) that only occur once.">
+			<option value="yes">Yes</option>
+			<option value="no" selected="true">No</option>
+			<option value="keep">Keep uniques and filter out the duplicates</option>
+		</param>
+	</inputs>
+	<outputs>
+		<data format="html" name="out_file" label = "Mutation analysis on ${in_file.name}"/>
+		<data format="tabular" name="naive_output" label = "Naive input data from ${in_file.name}" >
+		    <filter>naive_output_cond['naive_output'] == "yes"</filter>
+		</data>
+	</outputs>
+	<help>
+		Takes an IMGT zip (http://www.imgt.org/HighV-QUEST/search.action) file and creates a summarization of the mutation analysis.
+	</help>
+	<requirements>
+    <requirement type="package" version="1.0">blastn</requirement>
+	</requirements>
+</tool>