<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
	</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="no_results" selected="true">Remove "No results"</option>
			<option value="no_result_unproductive">Remove "No results" and "unproductive"</option>
			<option value="dont_remove">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="V_subclass">V + 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>
		
	</inputs>
	<outputs>
		<data format="html" name="out_file" label = "Mutation analysis on ${in_file.name}"/>
	</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>