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<tool id="change_o_define_clones_galaxy" name="Define Clones" version="1.0">
	<description>Change-O</description>
	<command interpreter="bash">
		#if $input_type.input_type_select=="bygroup"
			define_clones.sh bygroup $input $input_type.mode $input_type.act $input_type.model $input_type.norm $input_type.sym $input_type.link $input_type.dist $out_file $out_file2
		#else
			define_clones.sh hclust $input $input_type.method $out_file $out_file2
		#end if
	</command>
	<inputs>
		<param name="input" type="data" format="tabular" label="A Change-O DB file" />
		<conditional name="input_type">
			<param name="input_type_select" type="select" label="Input type">
				<option value="bygroup" selected="true">Define clones by V assignment, J assignment and junction length</option>
				<option value="hclust">Define clones by specified distance metric on CDR3s and cutting of hierarchical clustering tree</option>
			</param>
			<when value="bygroup">
				<param name="mode" type="select" label="Specifies whether to use the V(D)J allele or gene for initial grouping.">
					<option value="allele">Allele</option>
					<option value="gene" selected="true">Gene</option>
				</param>
				<param name="act" type="select" label="Specifies how to handle multiple V(D)J assignments for initial grouping.">
					<option value="first" selected="true">First</option>
					<option value="set">Set</option>
				</param>
				<param name="model" type="select" label="Specifies which substitution model to use for calculating distance between sequences.">
					<option value="aa">AA hamming distance</option>
					<option value="ham" selected="true">Nucleotide hamming distance</option>
					<option value="m1n">Mouse single nucleotide (Smith et al, 1996)</option>
					<option value="hs1f">Human single nucleotide (Yaari et al, 2013)</option>
					<option value="hs5f">Human S5F (Yaari et al, 2013)</option>
				</param>
				<param name="norm" type="select" label="Specifies how to normalize distances.">
					<option value="none" selected="true">Do not normalize</option>
					<option value="mut">Normalize by number of mutations</option>
					<option value="len">Normalize by length</option>
				</param>
				<param name="sym" type="select" label="Specifies how to combine asymmetric distances.">
					<option value="avg">Average</option>
					<option value="min" selected="true">Minimum</option>
				</param>
				<param name="link" type="select" label="Type of linkage to use for hierarchical clustering.">
					<option value="single">Single</option>
					<option value="average">Average</option>
					<option value="complete" selected="true">Complete</option>
				</param>
				<param name="dist" size="4" type="float" value="0.0" label="The distance threshold for clonal grouping" />
			</when>
			<when value="hclust">
				<param name="method" type="select" label="Specifies which cloning method to use for calculating distance between CDR3s">
					<option value="chen2010" selected="true">Chen et al 2010</option>
					<option value="ademokun2011">Ademokun et al 2011</option>
				</param>
			</when>
		</conditional>
	</inputs>
	<outputs>
		<data format="tabular" name="out_file" label = "Change-o DB clones ${input.name}"/>
		<data format="tabular" name="out_file2" label = "Change-o DB clones info ${input.name}"/>
	</outputs>
	<citations>
		<citation type="doi">10.1093/bioinformatics/btv359</citation>
	</citations>
	<help>
			
	
	</help>
</tool>