<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>
		</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>