diff baseline.xml @ 2:94fada165724 draft

Uploaded

--- a/baseline.xml	Tue Jul 15 09:00:24 2014 -0400
+++ b/baseline.xml	Wed Aug 13 07:32:38 2014 -0400
@@ -1,10 +1,24 @@
 <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
+		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 $out_file
 	</command>
 	<inputs>
-		<param name="in_file" format="fasta" type="data" label="Data to Process" />
+		<repeat name="inputs" title="inputs" min="1" default="1">
+			<param name="in_file" type="data" label="Input excel or IMGT zip file" />
+			<param name="id" type="text" label="ID (alpha-numeric, no spaces)" />
+		</repeat>
+		<param name="reference" type="data" format="fasta" label="Reference fasta file" />
 		<param name="ss" type="select" label="Selection Statistic">
 			<option value="1">Focused</option>
 			<option value="2">Local</option>
@@ -14,13 +28,13 @@
 			<option value="2">Mouse</option>
 		</param>
 		<param name="substitution" type="select" label="Substitution Model">
+			<option value="1">Smith DS et al. 1996</option>
 			<option value="0">Uniform substitution</option>
-			<option value="1">Smith DS et al. 1996</option>
 			<option value="5">FiveS</option>
 		</param>
 		<param name="mutability" type="select" label="Mutability Model">
+			<option value="1">Tri-nucleotide (Shapiro GS et al. 2002)</option>
 			<option value="0">Uniform mutability</option>
-			<option value="1">Tri-nucleotide (Shapiro GS et al. 2002)</option>
 			<option value="5">FiveS</option>
 		</param>
 		<param name="clonal" type="select" label="Sequences are clonal">
@@ -33,13 +47,12 @@
 			<option value="1">Try and fix Indels</option>
 		</param>
 		<param name="boundaries" type="select" label="FWR/CDR3 Boundaries">
+			<option value="1:26:38:55:65:104:-">IMGT® No CDR3</option>
 			<option value="1:26:38:55:65:104:116">IMGT®</option>
-			<option value="1:26:38:55:65:104:-">IMGT® No CDR3</option>
 		</param>
 	</inputs>
 	<outputs>
-		<data format="tabular" name="out_file" label = "${tool.name} on ${on_string}: result"/>
-		<data format="data" name="out_file2" label = "${tool.name} on ${on_string}: RData"/>
+		<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.