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<tool id="baseline_bayesian_estimation" name="Baseline" version="1.0">
	<description>Bayesian Estimation of Antigen-Driven Selection</description>
	<command interpreter="bash">
		wrapper.sh $ss $species $substitution $mutability $clonal $fixindels "$boundaries" "
		#for $i, $input in enumerate($inputs)
 ${input.in_file}
		#end for 
		"
		"
		#for $i, $input in enumerate($inputs)
 ${input.id}
		#end for 
		"
    $reference $out_file "$selection"
	</command>
	<inputs>
		<repeat name="inputs" title="inputs" min="1" default="1">
			<param name="in_file" type="data" label="Input excel or IMGT zip file" />
			<param name="id" type="text" label="ID (alpha-numeric, no spaces)" />
		</repeat>
		<param name="reference" type="data" format="fasta" label="Reference fasta file" />
		<param name="ss" type="select" label="Selection Statistic">
			<option value="1">Focused</option>
			<option value="2">Local</option>
		</param>
		<param name="species" type="select" label="SHM Targeting Model">
			<option value="1">Human</option>
			<option value="2">Mouse</option>
		</param>
		<param name="substitution" type="select" label="Substitution Model">
			<option value="1">Smith DS et al. 1996</option>
			<option value="0">Uniform substitution</option>
			<option value="5">FiveS</option>
		</param>
		<param name="mutability" type="select" label="Mutability Model">
			<option value="1">Tri-nucleotide (Shapiro GS et al. 2002)</option>
			<option value="0">Uniform mutability</option>
			<option value="5">FiveS</option>
		</param>
		<param name="clonal" type="select" label="Sequences are clonal">
			<option value="0">Independent sequences</option>
			<option value="1">Clonally related</option>
			<option value="2">Clonally related and only non-terminal mutations</option>
		</param>
		<param name="fixindels" type="select" label="Fix Indels">
			<option value="0">Do Nothing</option>
			<option value="1">Try and fix Indels</option>
		</param>
		<param name="boundaries" type="select" label="FWR/CDR3 Boundaries">
			<option value="1:26:38:55:65:104:-">IMGT® No CDR3</option>
			<option value="1:26:38:55:65:104:116">IMGT®</option>
		</param>
		<param name="selection" type="select" label="Unique Selection Definition">
			<option value="VGene,AA.JUNCTION">VGene, AA CDR3</option>
			<option value="VGene,JGene,AA.JUNCTION">VGene, JGene, AA CDR3</option>
			<option value="VGene,DGene,JGene,AA.JUNCTION">VGene, DGene, JGene, AA CDR3</option>
			<option value="Sequence.ID">None</option>
		</param>
	</inputs>
	<outputs>
		<data format="pdf" name="out_file" label = "Baseline on ${on_string}"/>
	</outputs>
	<help>
			Gur Yaari; Mohamed Uduman; Steven H. Kleinstein. Quantifying selection in high-throughput Immunoglobulin sequencing data sets. Nucleic Acids Res. 2012 May 27.

			Mohamed Uduman; Gur Yaari; Uri Hershberg; Mark J. Shlomchik; Steven H. Kleinstein. Detecting selection in immunoglobulin sequences. Nucleic Acids Res. 2011 Jul;39(Web Server issue):W499-504.
	
	</help>
</tool>