<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_ca $naive_output_cg $naive_output_cm $filter_uniques $class_filter
	</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="filter_uniques" type="select" label="Filter unique sequences" help="See below for an example.">
			<option value="yes">Remove uniques (CDR1 + FR2 + CDR2 + FR3 + CDR3)</option>
			<option value="yes_c">Remove uniques (CDR1 + FR2 + CDR2 + FR3 + CDR3 + C)</option>
			<option value="keep">Keep uniques (CDR1 + FR2 + CDR2 + FR3 + CDR3)</option>
			<option value="keep_c">Keep uniques (CDR1 + FR2 + CDR2 + FR3 + CDR3 + C)</option>
			<option value="no" selected="true">No</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>
		<param name="class_filter" type="select" label="Class/Sublass filter" help="" >
			<option value="70_70" selected="true">>70% class and >70% subclass</option>
			<option value="70_0">>70% class</option>
			<option value="60_0">>60% class</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>
	</inputs>
	<outputs>
		<data format="html" name="out_file" label = "Mutation analysis on ${in_file.name}"/>
		<data format="tabular" name="naive_output_ca" label = "Naive CA input data from ${in_file.name}" >
		    <filter>naive_output_cond['naive_output'] == "yes"</filter>
		</data>
		<data format="tabular" name="naive_output_cg" label = "Naive CG input data from ${in_file.name}" >
		    <filter>naive_output_cond['naive_output'] == "yes"</filter>
		</data>
		<data format="tabular" name="naive_output_cm" label = "Naive CM 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.  
		
		+--------------------------+
		|       unique filter      |
		+--------+--------+--------+
		| values | remove | keep   |
		+--------+--------+--------+
		|   A    |   A    |   A    |
		+--------+--------+--------+
		|   A    |   B    |   B    |
		+--------+--------+--------+
		|   B    |   D    |   C    |
		+--------+--------+--------+
		|   B    |        |   D    |
		+--------+--------+--------+
		|   C    |        |        |
		+--------+--------+--------+
		|   D    |        |        |
		+--------+--------+--------+
		|   D    |        |        |
		+--------+--------+--------+
		
	</help>
	<requirements>
    <requirement type="package" version="1.0">blastn</requirement>
	</requirements>
</tool>