# HG changeset patch
# User davidvanzessen
# Date 1470315587 14400
# Node ID 326165da9ece53559ebde307d511b35d29bbc1b5
# Parent  dda9b2e72e2b2ee0c5741295797363f1fa5c53db
Uploaded

diff -r dda9b2e72e2b -r 326165da9ece create_germlines.sh
--- a/create_germlines.sh	Tue May 03 09:52:21 2016 -0400
+++ b/create_germlines.sh	Thu Aug 04 08:59:47 2016 -0400
@@ -16,7 +16,7 @@
 
 mkdir $PWD/outdir
 
-#/home/galaxy/anaconda3/bin/python $dir/CreateGermlines.py -d $PWD/input.tab -r $germline --outdir $PWD/outdir --outname output -g $type $cloned
-/data/users/david/anaconda3/bin/python $dir/CreateGermlines.py -d $PWD/input.tab -r $dir/IMGT_Human_IGH[VDJ].fasta --outdir $PWD/outdir --outname output -g $type $cloned
+/home/galaxy/anaconda3/bin/python $dir/CreateGermlines.py -d $PWD/input.tab -r $dir/IMGT_Human_IGH[VDJ].fasta --outdir $PWD/outdir --outname output -g $type $cloned
+#/data/users/david/anaconda3/bin/python $dir/CreateGermlines.py -d $PWD/input.tab -r $dir/IMGT_Human_IGH[VDJ].fasta --outdir $PWD/outdir --outname output -g $type $cloned
 
 mv $PWD/outdir/output_germ-pass.tab $output
diff -r dda9b2e72e2b -r 326165da9ece define_clones.r
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/define_clones.r	Thu Aug 04 08:59:47 2016 -0400
@@ -0,0 +1,14 @@
+args <- commandArgs(trailingOnly = TRUE)
+
+input=args[1]
+output=args[2]
+
+change.o = read.table(input, header=T, sep="\t", quote="", stringsAsFactors=F)
+
+freq = data.frame(table(change.o$CLONE))
+freq2 = data.frame(table(freq$Freq))
+freq2$final = round(freq2$Freq / as.numeric(freq2$Var1), 2)
+
+names(freq2) = c("freq", "freq.of.freq", "divided")
+
+write.table(x=freq2, file=output, sep="\t",quote=F,row.names=F,col.names=T)
diff -r dda9b2e72e2b -r 326165da9ece define_clones.sh
--- a/define_clones.sh	Tue May 03 09:52:21 2016 -0400
+++ b/define_clones.sh	Thu Aug 04 08:59:47 2016 -0400
@@ -19,13 +19,21 @@
 	link=$8
 	dist=$9
 	output=${10}
+	output2=${11}
 	
-	/data/users/david/anaconda3/bin/python $dir/DefineClones.py bygroup -d $PWD/input.tab --nproc 4 --outdir $PWD/outdir --outname output --mode $mode --act $act --model $model --dist $dist --norm $norm --sym $sym --link $link
+	#/data/users/david/anaconda3/bin/python $dir/DefineClones.py bygroup -d $PWD/input.tab --nproc 4 --outdir $PWD/outdir --outname output --mode $mode --act $act --model $model --dist $dist --norm $norm --sym $sym --link $link
+	/home/galaxy/anaconda3/bin/python $dir/DefineClones.py bygroup -d $PWD/input.tab --nproc 4 --outdir $PWD/outdir --outname output --mode $mode --act $act --model $model --dist $dist --norm $norm --sym $sym --link $link
+	
+	Rscript $dir/define_clones.r $PWD/outdir/output_clone-pass.tab $output2 2>&1
 else
 	method=$3
 	output=$4
+	output2=$5
 	
-	/data/users/david/anaconda3/bin/python $dir/DefineClones.py hclust -d $PWD/input.tab --nproc 4 --outdir $PWD/outdir --outname output --method $method
+	#/data/users/david/anaconda3/bin/python $dir/DefineClones.py hclust -d $PWD/input.tab --nproc 4 --outdir $PWD/outdir --outname output --method $method
+	/home/galaxy/anaconda3/bin/python $dir/DefineClones.py hclust -d $PWD/input.tab --nproc 4 --outdir $PWD/outdir --outname output --method $method
+	
+	Rscript $dir/define_clones.r $PWD/outdir/output_clone-pass.tab $output2 2>&1
 fi
 
 cp $PWD/outdir/output_clone-pass.tab $output
diff -r dda9b2e72e2b -r 326165da9ece define_clones.xml
--- a/define_clones.xml	Tue May 03 09:52:21 2016 -0400
+++ b/define_clones.xml	Thu Aug 04 08:59:47 2016 -0400
@@ -2,9 +2,9 @@
 	<description>Change-O</description>
 	<command interpreter="bash">
 		#if $input_type.input_type_select=="bygroup"
-			define_clones.sh bygroup $input $input_type.mode $input_type.act $input_type.model $input_type.norm $input_type.sym $input_type.link $input_type.dist $out_file
+			define_clones.sh bygroup $input $input_type.mode $input_type.act $input_type.model $input_type.norm $input_type.sym $input_type.link $input_type.dist $out_file $out_file2
 		#else
-			define_clones.sh hclust $input $input_type.method $out_file
+			define_clones.sh hclust $input $input_type.method $out_file $out_file2
 		#end if
 	</command>
 	<inputs>
@@ -56,6 +56,7 @@
 	</inputs>
 	<outputs>
 		<data format="tabular" name="out_file" label = "Change-o DB clones ${input.name}"/>
+		<data format="tabular" name="out_file2" label = "Change-o DB clones info ${input.name}"/>
 	</outputs>
 	<citations>
 		<citation type="doi">10.1093/bioinformatics/btv359</citation>
diff -r dda9b2e72e2b -r 326165da9ece makedb.sh
--- a/makedb.sh	Tue May 03 09:52:21 2016 -0400
+++ b/makedb.sh	Thu Aug 04 08:59:47 2016 -0400
@@ -27,6 +27,7 @@
 
 mkdir $PWD/outdir
 
-/data/users/david/anaconda3/bin/python $dir/MakeDb.py imgt -i $input --outdir $PWD/outdir --outname output $noparse $scores $regions
+#/data/users/david/anaconda3/bin/python $dir/MakeDb.py imgt -i $input --outdir $PWD/outdir --outname output $noparse $scores $regions
+/home/galaxy/anaconda3/bin/python $dir/MakeDb.py imgt -i $input --outdir $PWD/outdir --outname output $noparse $scores $regions
 
 mv $PWD/outdir/output_db-pass.tab $output