# HG changeset patch
# User davidvanzessen
# Date 1433235743 14400
# Node ID 525b58fc8622d37b5c6d3104918b283c34f05211
# Parent  45a5e3bd9df49c9bd5f96aa00fb98399bb2ef2c3
Uploaded

diff -r 45a5e3bd9df4 -r 525b58fc8622 baseline.xml
--- a/baseline.xml	Mon Aug 18 05:54:51 2014 -0400
+++ b/baseline.xml	Tue Jun 02 05:02:23 2015 -0400
@@ -46,10 +46,7 @@
 			<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:-">IMGT® No CDR3</option>
-			<option value="1:26:38:55:65:104:116">IMGT®</option>
-		</param>
+		<param name="boundaries" type="text" value="1:26:38:55:65:104:116" 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>
@@ -64,6 +61,12 @@
 			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>
diff -r 45a5e3bd9df4 -r 525b58fc8622 wrapper.sh
--- a/wrapper.sh	Mon Aug 18 05:54:51 2014 -0400
+++ b/wrapper.sh	Tue Jun 02 05:02:23 2015 -0400
@@ -68,6 +68,8 @@
 done
 workdir="$PWD"
 cd $dir
+echo "file: ${inputs[0]}"
+#Rscript --verbose $dir/Baseline_Main.r $testID $species $substitutionModel $mutabilityModel $clonal $fixIndels $region ${inputs[0]} $workdir/ $outID 2>&1
 Rscript --verbose $dir/Baseline_Main.r $testID $species $substitutionModel $mutabilityModel $clonal $fixIndels $region $fasta $workdir/ $outID 2>&1
 
 echo "$workdir/${outID}.txt"