# HG changeset patch
# User davidvanzessen
# Date 1471436215 14400
# Node ID 6fdafffd7f0fe881d6ab5c2cd0725976dd2767f0
# Parent  a59de79f6c0ff48d6c6ed1ac30dc91b19b3820d7
Uploaded

diff -r a59de79f6c0f -r 6fdafffd7f0f report_clonality/r_wrapper.sh
--- a/report_clonality/r_wrapper.sh	Mon Aug 08 08:53:33 2016 -0400
+++ b/report_clonality/r_wrapper.sh	Wed Aug 17 08:16:55 2016 -0400
@@ -89,6 +89,7 @@
 	fi
 done
 echo "</title><script type='text/javascript' src='jquery-1.11.0.min.js'></script>" >> $outputFile
+echo "<link rel='stylesheet' href='http://yui.yahooapis.com/pure/0.6.0/pure-min.css'>" >> $outputFile
 echo "<script type='text/javascript' src='tabber.js'></script>" >> $outputFile
 echo "<script type='text/javascript' src='script.js'></script>" >> $outputFile
 echo "<link rel='stylesheet' type='text/css' href='style.css'></head>" >> $outputFile
@@ -158,8 +159,8 @@
 		if [[ "${clonality_method}" == "old" ]] ; then
 			echo "in old"
 			clonalityScore="$(cat $outputDir/ClonalityScore_$sample.csv)"
-			echo "<div class='tabbertab' title='$sample'><table border='1'>" >> $outputFile
-			echo "<tr><td colspan='4'>Clonality Score: $clonalityScore</td></tr>" >> $outputFile
+			echo "<div class='tabbertab' title='$sample'><table class='pure-table pure-table-striped'>" >> $outputFile
+			echo "<thead><tr><th colspan='4'>Clonality Score: $clonalityScore</th></tr></thead>" >> $outputFile
 
 			#replicate,reads,squared
 			echo "<tr><td>Replicate ID</td><td>Number of Reads</td><td>Reads Squared</td><td></td></tr>" >> $outputFile
@@ -207,28 +208,28 @@
 #if [[ "$hasJunctionData" == "Yes" ]] ; then
 if [ -a "$outputDir/junctionAnalysisProd_mean.csv" ] ; then
 	echo "<div class='tabbertab' title='Junction Analysis'>" >> $outputFile
-	echo "<table border='1' id='junction_table'> <caption>Productive mean</caption><thead><tr><th>Sample</th><th>count</th><th>V.DEL</th><th>P1</th><th>N1</th><th>P2</th><th>DEL.D</th><th>D.DEL</th><th>P3</th><th>N2</th><th>P4</th><th>DEL.J</th><th>Total.Del</th><th>Total.N</th><th>Total.P</th><thead></tr><tbody>" >> $outputFile
+	echo "<table class='pure-table pure-table-striped' id='junction_table'> <caption>Productive mean</caption><thead><tr><th>Sample</th><th>count</th><th>V.DEL</th><th>P1</th><th>N1</th><th>P2</th><th>DEL.D</th><th>D.DEL</th><th>P3</th><th>N2</th><th>P4</th><th>DEL.J</th><th>Total.Del</th><th>Total.N</th><th>Total.P</th><thead></tr><tbody>" >> $outputFile
 	while IFS=, read Sample unique VDEL P1 N1 P2 DELD DDEL P3 N2 P4 DELJ TotalDel TotalN TotalP
 	do
 		echo "<tr><td>$Sample</td><td>$unique</td><td>$VDEL</td><td>$P1</td><td>$N1</td><td>$P2</td><td>$DELD</td><td>$DDEL</td><td>$P3</td><td>$N2</td><td>$P4</td><td>$DELJ</td><td>$TotalDel</td><td>$TotalN</td><td>$TotalP</td></tr>" >> $outputFile
 	done < $outputDir/junctionAnalysisProd_mean.csv
 	echo "</tbody></table>" >> $outputFile
 	
-	echo "<table border='1' id='junction_table'> <caption>Unproductive mean</caption><thead><tr><th>Sample</th><th>count</th><th>V.DEL</th><th>P1</th><th>N1</th><th>P2</th><th>DEL.D</th><th>D.DEL</th><th>P3</th><th>N2</th><th>P4</th><th>DEL.J</th><th>Total.Del</th><th>Total.N</th><th>Total.P</th><thead></tr><tbody>" >> $outputFile
+	echo "<table class='pure-table pure-table-striped' id='junction_table'> <caption>Unproductive mean</caption><thead><tr><th>Sample</th><th>count</th><th>V.DEL</th><th>P1</th><th>N1</th><th>P2</th><th>DEL.D</th><th>D.DEL</th><th>P3</th><th>N2</th><th>P4</th><th>DEL.J</th><th>Total.Del</th><th>Total.N</th><th>Total.P</th><thead></tr><tbody>" >> $outputFile
 	while IFS=, read Sample unique VDEL P1 N1 P2 DELD DDEL P3 N2 P4 DELJ TotalDel TotalN TotalP
 	do
 		echo "<tr><td>$Sample</td><td>$unique</td><td>$VDEL</td><td>$P1</td><td>$N1</td><td>$P2</td><td>$DELD</td><td>$DDEL</td><td>$P3</td><td>$N2</td><td>$P4</td><td>$DELJ</td><td>$TotalDel</td><td>$TotalN</td><td>$TotalP</td></tr>" >> $outputFile
 	done < $outputDir/junctionAnalysisUnProd_mean.csv
 	echo "</tbody></table>" >> $outputFile
 	
-	echo "<table border='1' id='junction_table'> <caption>Productive median</caption><thead><tr><th>Sample</th><th>count</th><th>V.DEL</th><th>P1</th><th>N1</th><th>P2</th><th>DEL.D</th><th>D.DEL</th><th>P3</th><th>N2</th><th>P4</th><th>DEL.J</th><th>Total.Del</th><th>Total.N</th><th>Total.P</th><thead></tr><tbody>" >> $outputFile
+	echo "<table class='pure-table pure-table-striped' id='junction_table'> <caption>Productive median</caption><thead><tr><th>Sample</th><th>count</th><th>V.DEL</th><th>P1</th><th>N1</th><th>P2</th><th>DEL.D</th><th>D.DEL</th><th>P3</th><th>N2</th><th>P4</th><th>DEL.J</th><th>Total.Del</th><th>Total.N</th><th>Total.P</th><thead></tr><tbody>" >> $outputFile
 	while IFS=, read Sample unique VDEL P1 N1 P2 DELD DDEL P3 N2 P4 DELJ TotalDel TotalN TotalP
 	do
 		echo "<tr><td>$Sample</td><td>$unique</td><td>$VDEL</td><td>$P1</td><td>$N1</td><td>$P2</td><td>$DELD</td><td>$DDEL</td><td>$P3</td><td>$N2</td><td>$P4</td><td>$DELJ</td><td>$TotalDel</td><td>$TotalN</td><td>$TotalP</td></tr>" >> $outputFile
 	done < $outputDir/junctionAnalysisProd_median.csv
 	echo "</tbody></table>" >> $outputFile
 	
-	echo "<table border='1' id='junction_table'> <caption>Unproductive median</caption><thead><tr><th>Sample</th><th>count</th><th>V.DEL</th><th>P1</th><th>N1</th><th>P2</th><th>DEL.D</th><th>D.DEL</th><th>P3</th><th>N2</th><th>P4</th><th>DEL.J</th><th>Total.Del</th><th>Total.N</th><th>Total.P</th><thead></tr><tbody>" >> $outputFile
+	echo "<table class='pure-table pure-table-striped' id='junction_table'> <caption>Unproductive median</caption><thead><tr><th>Sample</th><th>count</th><th>V.DEL</th><th>P1</th><th>N1</th><th>P2</th><th>DEL.D</th><th>D.DEL</th><th>P3</th><th>N2</th><th>P4</th><th>DEL.J</th><th>Total.Del</th><th>Total.N</th><th>Total.P</th><thead></tr><tbody>" >> $outputFile
 	while IFS=, read Sample unique VDEL P1 N1 P2 DELD DDEL P3 N2 P4 DELJ TotalDel TotalN TotalP
 	do
 		echo "<tr><td>$Sample</td><td>$unique</td><td>$VDEL</td><td>$P1</td><td>$N1</td><td>$P2</td><td>$DELD</td><td>$DDEL</td><td>$P3</td><td>$N2</td><td>$P4</td><td>$DELJ</td><td>$TotalDel</td><td>$TotalN</td><td>$TotalP</td></tr>" >> $outputFile
@@ -249,8 +250,8 @@
 echo "</div></div>" >> $outputFile
 
 echo "<div class='tabbertab' title='Downloads'>" >> $outputFile
-echo "<table border='1'>" >> $outputFile
-echo "<tr><th>Description</th><th>Link</th></tr>" >> $outputFile
+echo "<table class='pure-table pure-table-striped'>" >> $outputFile
+echo "<thead><tr><th>Description</th><th>Link</th></tr></thead>" >> $outputFile
 echo "<tr><td>The dataset used to generate the frequency graphs and the heatmaps (Unique based on clonaltype, $clonalType)</td><td><a href='allUnique.csv'>Download</a></td></tr>" >> $outputFile
 echo "<tr><td>The dataset used to calculate clonality score (Unique based on clonaltype, $clonalType)</td><td><a href='clonalityComplete.csv'>Download</a></td></tr>" >> $outputFile
 
diff -r a59de79f6c0f -r 6fdafffd7f0f report_clonality_igg.xml
--- a/report_clonality_igg.xml	Mon Aug 08 08:53:33 2016 -0400
+++ b/report_clonality_igg.xml	Wed Aug 17 08:16:55 2016 -0400
@@ -11,11 +11,12 @@
 		<param name="in_file" format="tabular" type="data" label="Data to Process" />
 		<param name="clonaltype" type="select" label="Clonal Type Definition (Needed for clonality calculation)">
 			<option value="none">Don't remove duplicates based on clonaltype</option>
-			<option value="Top.V.Gene,CDR3.Seq">Top.V.Gene, CDR3.Seq</option>
+			<option value="Top.V.Gene,CDR3.Seq">Top.V.Gene, CDR3.AA.Seq</option>
 			<option value="Top.V.Gene,CDR3.Seq.DNA">Top.V.Gene, CDR3.Seq.DNA</option>
-			<option value="Top.V.Gene,Top.J.Gene,CDR3.Seq">Top.V.Gene, Top.J.Gene, CDR3.Seq</option>
+			<option value="Top.V.Gene,Top.J.Gene,CDR3.Seq">Top.V.Gene, Top.J.Gene, CDR3.AA.Seq</option>
 			<option value="Top.V.Gene,Top.J.Gene,CDR3.Seq.DNA">Top.V.Gene, Top.J.Gene, CDR3.Seq.DNA</option>
 			<option value="Top.V.Gene,Top.D.Gene,Top.J.Gene,CDR3.Seq.DNA">Top.V.Gene, Top.D.Gene, Top.J.Gene, CDR3.Seq.DNA</option>
+			<option value="Top.V.Gene,Top.D.Gene,Top.J.Gene,CDR3.Seq">Top.V.Gene, Top.D.Gene, Top.J.Gene, CDR3.AA.DNA</option>
 		</param>
 		
 		<conditional name="gene_selection" >
@@ -85,7 +86,7 @@
 			</when>
 		</conditional>
 		
-		<param name="filterproductive" type="select" label="Filter out the unproductive sequences">
+		<param name="filterproductive" type="select" label="Remove the unproductive sequences from graphs ">
 			<option value="yes">Yes</option>
 			<option value="no">No</option>
 		</param>