--- a/tmp/baseline/baseline.xml	Wed Jun 08 03:54:49 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,73 +0,0 @@
-<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" "$out_table"
-	</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="text" value="25:26:38:55:65:104:-" size="40" label="Custom Boundaries (FWR1Start:FWR1End:CDR1End:FWR2End:CDR3End:FWR3End:CDR3End)" />
-		<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 PDF on ${on_string}"/>
-		<data format="tabular" name="out_table" label = "Baseline Table 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.
-			
-			**Boundaries**
-			
-			IMGT® No CDR3: "1:26:38:55:65:104:-"
-			
-			IMGT®: "1:26:38:55:65:104:116"
-	
-	</help>
-</tool>