diff tmp/baseline/baseline.xml @ 95:a66eb1c5374c draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tmp/baseline/baseline.xml	Wed Jun 08 03:54:49 2016 -0400
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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" "$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>