# HG changeset patch
# User davidvanzessen
# Date 1462349209 14400
# Node ID 2d08a1353145198a27ae431267d7c90cf3b26ce1
# Parent  7eeb7b808af919ba7777d85d3df9770f8c934fcc
Uploaded

diff -r 7eeb7b808af9 -r 2d08a1353145 baseline.xml
--- a/baseline.xml	Tue Mar 22 05:13:24 2016 -0400
+++ b/baseline.xml	Wed May 04 04:06:49 2016 -0400
@@ -11,7 +11,7 @@
  ${input.id}
 		#end for 
 		"
-    $reference $out_file "$selection"
+    $reference $out_file "$selection" "$out_table"
 	</command>
 	<inputs>
 		<repeat name="inputs" title="inputs" min="1" default="1">
@@ -55,7 +55,8 @@
 		</param>
 	</inputs>
 	<outputs>
-		<data format="pdf" name="out_file" label = "Baseline on ${on_string}"/>
+		<data format="pdf" name="out_file" label = "Baseline PDF on ${on_string}"/>
+		<data format="tabular" name="out_table" label = "Baseline Table on ${on_string}"/>
 	</outputs>
 	<help>
 			Gur Yaari; Mohamed Uduman; Steven H. Kleinstein. Quantifying selection in high-throughput Immunoglobulin sequencing data sets. Nucleic Acids Res. 2012 May 27.
diff -r 7eeb7b808af9 -r 2d08a1353145 wrapper.sh
--- a/wrapper.sh	Tue Mar 22 05:13:24 2016 -0400
+++ b/wrapper.sh	Wed May 04 04:06:49 2016 -0400
@@ -16,8 +16,11 @@
 ref=${10}
 output=${11}
 selection=${12}
+output_table=${13}
 outID="result"
 
+echo "$PWD"
+
 echo "testID = $testID"
 echo "species = $species"
 echo "substitutionModel = $substitutionModel"
@@ -89,8 +92,8 @@
 
 cd $dir
 Rscript --verbose $dir/comparePDFs.r $workdir/${outID}.RData $output ${rows[@]} 2>&1
+cp $workdir/result.txt ${output_table}
 
 
 
 
-