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<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 $empty_region_filter
	</command>
	<inputs>
		<param name="in_file" type="data" label="IMGT zip file to be analysed" />
		<param name="method" type="select" label="Method of identification of C region" 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="remove">Remove uniques (Based on nucleotide sequence + C)</option>
			<option value="keep">Keep uniques (Based on nucleotide sequence + C)</option>
			<option value="no" selected="true">No</option>
		</param>
		<param name="unique" type="select" label="Remove duplicates based on" help="" >
			<option value="VGene,AA.JUNCTION,best_match" selected="true">Top.V.Gene, CDR3.AA.Seq, C region</option>			
			<option value="VGene,AA.JUNCTION">Top.V.Gene, CDR3.AA.Seq</option>
			<option value="AA.JUNCTION,best_match">CDR3.AA.Seq, C region</option>
			<option value="AA.JUNCTION">CDR3.AA.Seq</option>
			
			<option value="VGene,CDR3.IMGT.seq,best_match" selected="true">Top.V.Gene, CDR3.nt.Seq, C region</option>			
			<option value="VGene,CDR3.IMGT.seq">Top.V.Gene, CDR3.nt.Seq</option>
			<option value="CDR3.IMGT.seq,best_match">CDR3.nt.Seq, C region</option>
			<option value="CDR3.IMGT.seq">CDR3.nt.Seq</option>
			<option value="Sequence.ID">Don't remove duplicates</option>
		</param>
		<param name="class_filter" type="select" label="Class/Subclass filter" help="" >
			<option value="70_70" selected="true">>70% class and >70% subclass</option>
			<option value="60_55">>60% class and >55% subclass</option>
			<option value="70_0">>70% class</option>
			<option value="60_0">>60% class</option>
		</param>
		<param name="empty_region_filter" type="select" label="Sequence starts at" help="" >
			<option value="FR1" selected="true">FR1: exclude empty CDR1,FR2,CDR2,FR3</option>
			<option value="CDR1">CDR1: exclude empty FR2,CDR2,FR3</option>
			<option value="FR2">FR2: exclude empty CDR2,FR3</option>
		</param>
		<conditional name="naive_output_cond">
			<param name="naive_output" type="select" label="Output new IMGT archives per class into your history?">
				<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="imgt_archive" name="naive_output_ca" label = "Naive CA input data from ${in_file.name}" >
		    <filter>naive_output_cond['naive_output'] == "yes"</filter>
		</data>
		<data format="imgt_archive" name="naive_output_cg" label = "Naive CG input data from ${in_file.name}" >
		    <filter>naive_output_cond['naive_output'] == "yes"</filter>
		</data>
		<data format="imgt_archive" name="naive_output_cm" label = "Naive CM input data from ${in_file.name}" >
		    <filter>naive_output_cond['naive_output'] == "yes"</filter>
		</data>
	</outputs>
	<citations>
		<citation type="doi">10.1093/nar/gks457</citation>
		<citation type="doi">10.1093/bioinformatics/btv359</citation>
		<citation type="doi">10.1186/1471-2105-10-421</citation>
	</citations>
	<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>