--- a/mutation_analysis.xml	Wed Apr 20 10:16:25 2016 -0400
+++ b/mutation_analysis.xml	Fri Apr 22 05:07:10 2016 -0400
@@ -1,7 +1,7 @@
 <tool id="mutation_analysis_shm" name="Mutation Analysis" version="1.0">
 	<description></description>
 	<command interpreter="bash">
-		wrapper.sh $in_file $method $out_file $out_file.files_path ${in_file.name} ${include_fr1} $functionality $unique $naive_output $filter_uniques $class_filter
+		wrapper.sh $in_file $method $out_file $out_file.files_path ${in_file.name} ${include_fr1} $functionality $unique $naive_output_ca $naive_output_cg $naive_output_cm $filter_uniques $class_filter
 	</command>
 	<inputs>
 		<param name="in_file" type="data" label="IMGT zip file to be analysed" />
@@ -47,7 +47,13 @@
 	</inputs>
 	<outputs>
 		<data format="html" name="out_file" label = "Mutation analysis on ${in_file.name}"/>
-		<data format="tabular" name="naive_output" label = "Naive input data from ${in_file.name}" >
+		<data format="tabular" name="naive_output_ca" label = "Naive CA input data from ${in_file.name}" >
+		    <filter>naive_output_cond['naive_output'] == "yes"</filter>
+		</data>
+		<data format="tabular" name="naive_output_cg" label = "Naive CG input data from ${in_file.name}" >
+		    <filter>naive_output_cond['naive_output'] == "yes"</filter>
+		</data>
+		<data format="tabular" name="naive_output_cm" label = "Naive CM input data from ${in_file.name}" >
 		    <filter>naive_output_cond['naive_output'] == "yes"</filter>
 		</data>
 	</outputs>

--- a/naive_output.r	Wed Apr 20 10:16:25 2016 -0400
+++ b/naive_output.r	Fri Apr 22 05:07:10 2016 -0400
@@ -2,7 +2,9 @@
 
 naive.file = args[1]
 shm.file = args[2]
-output.file = args[3]
+output.file.ca = args[3]
+output.file.cg = args[4]
+output.file.cm = args[5]
 
 naive = read.table(naive.file, sep="\t", header=T, quote="", fill=T)
 shm.merge = read.table(shm.file, sep="\t", header=T, quote="", fill=T)
@@ -14,10 +16,19 @@
 final.numeric = final[,sapply(final, is.numeric)]
 final.numeric[is.na(final.numeric)] = 0
 final[,sapply(final, is.numeric)] = final.numeric
-print(paste("nrow final:", nrow(final)))
-final2 = final
-final2$Sample = gsub("[0-9]", "", final2$Sample)
-final = rbind(final, final2)
-final$Replicate = 1
+
+final.ca = final[grepl("ca", final$Sample),]
+final.cg = final[grepl("cg", final$Sample),]
+final.cm = final[grepl("cm", final$Sample),]
+
+
 
-write.table(final, output.file, quote=F, sep="\t", row.names=F, col.names=T)
+#print(paste("nrow final:", nrow(final)))
+#final2 = final
+#final2$Sample = gsub("[0-9]", "", final2$Sample)
+#final = rbind(final, final2)
+#final$Replicate = 1
+
+write.table(final.ca, output.file.ca, quote=F, sep="\t", row.names=F, col.names=T)
+write.table(final.cg, output.file.cg, quote=F, sep="\t", row.names=F, col.names=T)
+write.table(final.cm, output.file.cm, quote=F, sep="\t", row.names=F, col.names=T)

--- a/wrapper.sh	Wed Apr 20 10:16:25 2016 -0400
+++ b/wrapper.sh	Fri Apr 22 05:07:10 2016 -0400
@@ -9,9 +9,11 @@
 include_fr1=$6
 functionality=$7
 unique=$8
-naive_output=$9
-filter_unique=${10}
-class_filter=${11}
+naive_output_ca=$9
+naive_output_cg=${10}
+naive_output_cm=${11}
+filter_unique=${12}
+class_filter=${13}
 mkdir $outdir
 
 echo "---------------- read parameters ----------------"
@@ -222,9 +224,9 @@
 then
 	echo "---------------- imgt_loader.r ----------------"
 	#python $dir/imgt_loader.py --summ $PWD/summary.txt --aa $PWD/aa.txt --junction $PWD/junction.txt --output $naive_output
-	Rscript --verbose $dir/imgt_loader.r $PWD/summary.txt $PWD/aa.txt $PWD/junction.txt ${naive_output} 2>&1
+	Rscript --verbose $dir/imgt_loader.r $PWD/summary.txt $PWD/aa.txt $PWD/junction.txt ${naive_output_ca} 2>&1
 	echo "---------------- naive_output.r ----------------"
-	Rscript $dir/naive_output.r $naive_output $outdir/merged.txt $naive_output 2>&1
+	Rscript $dir/naive_output.r $naive_output_ca $outdir/merged.txt $naive_output_ca $naive_output_cg $naive_output_cm 2>&1
 fi