--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/define_clones.xml	Tue May 03 09:52:21 2016 -0400
@@ -0,0 +1,67 @@
+<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
+		#else
+			define_clones.sh hclust $input $input_type.method $out_file
+		#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">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">First</option>
+					<option value="set" selected="true">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">Nucleotide hamming distance</option>
+					<option value="m1n">Mouse single nucleotide (Smith et al, 1996)</option>
+					<option value="hs1f" selected="true">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">Do not normalize</option>
+					<option value="mut">Normalize by number of mutations</option>
+					<option value="len" selected="true">Normalize by length</option>
+				</param>
+				<param name="sym" type="select" label="Specifies how to combine asymmetric distances.">
+					<option value="avg" selected="true">Average</option>
+					<option value="min">Minimum</option>
+				</param>
+				<param name="link" type="select" label="Type of linkage to use for hierarchical clustering.">
+					<option value="single" selected="true">Single</option>
+					<option value="average">Average</option>
+					<option value="complete">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}"/>
+	</outputs>
+	<citations>
+		<citation type="doi">10.1093/bioinformatics/btv359</citation>
+	</citations>
+	<help>
+			
+	
+	</help>
+</tool>