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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" $in_file $out_file.files_path result $out_file $out_file2
	</command>
	<inputs>
		<param name="in_file" format="fasta" type="data" label="Data to Process" />
		<param name="ss" type="select" label="Selection Statistic">
			<option value="1">Focused</option>
			<option value="2">Local</option>
		</param>
		<param name="species" type="select" label="SHM Targeting Model">
			<option value="1">Human</option>
			<option value="2">Mouse</option>
		</param>
		<param name="substitution" type="select" label="Substitution Model">
			<option value="0">Uniform substitution</option>
			<option value="1">Smith DS et al. 1996</option>
			<option value="5">FiveS</option>
		</param>
		<param name="mutability" type="select" label="Mutability Model">
			<option value="0">Uniform mutability</option>
			<option value="1">Tri-nucleotide (Shapiro GS et al. 2002)</option>
			<option value="5">FiveS</option>
		</param>
		<param name="clonal" type="select" label="Sequences are clonal">
			<option value="0">Independent sequences</option>
			<option value="1">Clonally related</option>
			<option value="2">Clonally related and only non-terminal mutations</option>
		</param>
		<param name="fixindels" type="select" label="Fix Indels">
			<option value="0">Do Nothing</option>
			<option value="1">Try and fix Indels</option>
		</param>
		<param name="boundaries" type="select" label="FWR/CDR3 Boundaries">
			<option value="1:26:38:55:65:104:116">IMGT®</option>
			<option value="1:26:38:55:65:104:-">IMGT® No CDR3</option>
		</param>
	</inputs>
	<outputs>
		<data format="tabular" name="out_file" label = "${tool.name} on ${on_string}: result"/>
		<data format="data" name="out_file2" label = "${tool.name} on ${on_string}: RData"/>
	</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>