# HG changeset patch
# User davidvanzessen
# Date 1473926073 14400
# Node ID 3ddd933dd7a29590e0650e4075777929d88250e2
# Parent  3d97839fda21128bda04189e260a558dc6c52eaa
Uploaded

diff -r 3d97839fda21 -r 3ddd933dd7a2 create_germlines.sh
--- a/create_germlines.sh	Mon Aug 15 10:06:24 2016 -0400
+++ b/create_germlines.sh	Thu Sep 15 03:54:33 2016 -0400
@@ -17,6 +17,7 @@
 mkdir $PWD/outdir
 
 #/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
+#/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
+python3 $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 $output
diff -r 3d97839fda21 -r 3ddd933dd7a2 create_germlines.xml
--- a/create_germlines.xml	Mon Aug 15 10:06:24 2016 -0400
+++ b/create_germlines.xml	Thu Sep 15 03:54:33 2016 -0400
@@ -6,8 +6,8 @@
 	<inputs>
 		<param name="input" type="data" label="Input IMGT zip file" />
 		<param name="type" type="select" label="Type" help="Specify type(s) of germlines to include full germline, germline with D-region masked, or germline for V-region only." >
-			<option value="dmask" selected="true">Full germline</option>
-			<option value="full">Masked D-region</option>
+			<option value="full" selected="true">Full germline</option>
+			<option value="dmask">Masked D-region</option>
 			<option value="vonly" >V-region only</option>
 		</param>
 		<param name="cloned" type="select" label="Cloned" help="Create one germline per clone" >
diff -r 3d97839fda21 -r 3ddd933dd7a2 define_clones.r
--- a/define_clones.r	Mon Aug 15 10:06:24 2016 -0400
+++ b/define_clones.r	Thu Sep 15 03:54:33 2016 -0400
@@ -8,16 +8,8 @@
 freq = data.frame(table(change.o$CLONE))
 freq2 = data.frame(table(freq$Freq))
 
-print(freq)
-
-print(freq2$Freq)
-
-print(freq2$Var1)
-
 freq2$final = as.numeric(freq2$Freq) * as.numeric(as.character(freq2$Var1))
 
-print(freq2)
-
 names(freq2) = c("Clone size", "Nr of clones", "Nr of sequences")
 
 write.table(x=freq2, file=output, sep="\t",quote=F,row.names=F,col.names=T)
diff -r 3d97839fda21 -r 3ddd933dd7a2 define_clones.sh
--- a/define_clones.sh	Mon Aug 15 10:06:24 2016 -0400
+++ b/define_clones.sh	Thu Sep 15 03:54:33 2016 -0400
@@ -6,7 +6,9 @@
 type=$1
 input=$2
 
-mkdir $PWD/outdir
+mkdir -p $PWD/outdir
+
+echo "defineclones: $PWD/outdir"
 
 cp $input $PWD/input.tab #file has to have a ".tab" extension
 
@@ -21,7 +23,7 @@
 	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
+	python3 $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
@@ -30,7 +32,7 @@
 	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
+	python3 $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
diff -r 3d97839fda21 -r 3ddd933dd7a2 define_clones.xml
--- a/define_clones.xml	Mon Aug 15 10:06:24 2016 -0400
+++ b/define_clones.xml	Thu Sep 15 03:54:33 2016 -0400
@@ -11,7 +11,7 @@
 		<param name="input" type="data" format="tabular" label="A Change-O DB file" />
 		<conditional name="input_type">
 			<param name="input_type_select" type="select" label="Input type">
-				<option value="bygroup">Define clones by V assignment, J assignment and junction length</option>
+				<option value="bygroup" selected="true">Define clones by V assignment, J assignment and junction length</option>
 				<option value="hclust">Define clones by specified distance metric on CDR3s and cutting of hierarchical clustering tree</option>
 			</param>
 			<when value="bygroup">
@@ -20,29 +20,29 @@
 					<option value="gene" selected="true">Gene</option>
 				</param>
 				<param name="act" type="select" label="Specifies how to handle multiple V(D)J assignments for initial grouping.">
-					<option value="first">First</option>
-					<option value="set" selected="true">Set</option>
+					<option value="first" selected="true">First</option>
+					<option value="set">Set</option>
 				</param>
 				<param name="model" type="select" label="Specifies which substitution model to use for calculating distance between sequences.">
 					<option value="aa">AA hamming distance</option>
-					<option value="ham">Nucleotide hamming distance</option>
+					<option value="ham" selected="true">Nucleotide hamming distance</option>
 					<option value="m1n">Mouse single nucleotide (Smith et al, 1996)</option>
-					<option value="hs1f" selected="true">Human single nucleotide (Yaari et al, 2013)</option>
+					<option value="hs1f">Human single nucleotide (Yaari et al, 2013)</option>
 					<option value="hs5f">Human S5F (Yaari et al, 2013)</option>
 				</param>
 				<param name="norm" type="select" label="Specifies how to normalize distances.">
-					<option value="none">Do not normalize</option>
+					<option value="none" selected="true">Do not normalize</option>
 					<option value="mut">Normalize by number of mutations</option>
-					<option value="len" selected="true">Normalize by length</option>
+					<option value="len">Normalize by length</option>
 				</param>
 				<param name="sym" type="select" label="Specifies how to combine asymmetric distances.">
-					<option value="avg" selected="true">Average</option>
-					<option value="min">Minimum</option>
+					<option value="avg">Average</option>
+					<option value="min" selected="true">Minimum</option>
 				</param>
 				<param name="link" type="select" label="Type of linkage to use for hierarchical clustering.">
-					<option value="single" selected="true">Single</option>
+					<option value="single">Single</option>
 					<option value="average">Average</option>
-					<option value="complete">Complete</option>
+					<option value="complete" selected="true">Complete</option>
 				</param>
 				<param name="dist" size="4" type="float" value="0.0" label="The distance threshold for clonal grouping" />
 			</when>
diff -r 3d97839fda21 -r 3ddd933dd7a2 makedb.sh
--- a/makedb.sh	Mon Aug 15 10:06:24 2016 -0400
+++ b/makedb.sh	Thu Sep 15 03:54:33 2016 -0400
@@ -27,7 +27,8 @@
 
 mkdir $PWD/outdir
 
-/data/users/david/anaconda3/bin/python $dir/MakeDb.py imgt -i $input --outdir $PWD/outdir --outname output $noparse $scores $regions
+python3 $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
diff -r 3d97839fda21 -r 3ddd933dd7a2 parsedb.sh
--- a/parsedb.sh	Mon Aug 15 10:06:24 2016 -0400
+++ b/parsedb.sh	Thu Sep 15 03:54:33 2016 -0400
@@ -12,21 +12,21 @@
 mkdir $PWD/outdir
 
 if [ "fasta" == "$action" ] ; then
-	/data/users/david/anaconda3/bin/python $dir/ParseDb.py fasta -d $input --outdir $PWD/outdir --outname output
+	python3 $dir/ParseDb.py fasta -d $input --outdir $PWD/outdir --outname output
 	mv $PWD/outdir/output_sequences.fasta $output
 elif [ "clip" == "$action" ] ; then
-	/data/users/david/anaconda3/bin/python $dir/ParseDb.py clip -d $input --outdir $PWD/outdir --outname output
+	python3 $dir/ParseDb.py clip -d $input --outdir $PWD/outdir --outname output
 	mv $PWD/outdir/output_sequences.fasta $output
 elif [ "split" == "$action" ] ; then
 	field="`cat $input 2> /dev/null | head -n 1 | cut -f$4 | tr '\n\r' ' '`"
 	label=$5
 	mkdir $PWD/split
-	/data/users/david/anaconda3/bin/python $dir/ParseDb.py split -d $input --outdir $PWD/split --outname output -f $field 
+	python3 $dir/ParseDb.py split -d $input --outdir $PWD/split --outname output -f $field 
 	#rename "s/output_${field}/$label/" $PWD/split/*
 elif [ "add" == "$action" ] ; then
 	field="`cat $input 2> /dev/null | head -n 1 | cut -f$4 | tr '\n\r' ' '`"
 	value=$5
-	/data/users/david/anaconda3/bin/python $dir/ParseDb.py add -d $input --outdir $PWD/outdir --outname output -f $field -u $value
+	python3 $dir/ParseDb.py add -d $input --outdir $PWD/outdir --outname output -f $field -u $value
 	mv $PWD/outdir/output_parse-add.tab $output
 elif [ "delete" == "$action" ] ; then
 	field="`cat $input 2> /dev/null | head -n 1 | cut -f$4 | tr '\n\r' ' '`"
@@ -37,20 +37,20 @@
 	else
 		regex=""
 	fi
-	/data/users/david/anaconda3/bin/python $dir/ParseDb.py delete -d $input --outdir $PWD/outdir --outname output -f $field -u $value --logic any $regex
+	python3 $dir/ParseDb.py delete -d $input --outdir $PWD/outdir --outname output -f $field -u $value --logic any $regex
 	mv $PWD/outdir/output_parse-delete.tab $output
 elif [ "drop" == "$action" ] ; then
 	field="`cat $input 2> /dev/null | head -n 1 | cut -f$4 | tr '\n\r' ' '`"
-	/data/users/david/anaconda3/bin/python $dir/ParseDb.py drop -d $input --outdir $PWD/outdir --outname output -f $field
+	python3 $dir/ParseDb.py drop -d $input --outdir $PWD/outdir --outname output -f $field
 	mv $PWD/outdir/output_parse-drop.tab $output
 elif [ "index" == "$action" ] ; then
 	field=$4
-	/data/users/david/anaconda3/bin/python $dir/ParseDb.py index -d $input --outdir $PWD/outdir --outname output -f $field
+	python3 $dir/ParseDb.py index -d $input --outdir $PWD/outdir --outname output -f $field
 	mv $PWD/outdir/output_parse-index.tab $output
 elif [ "rename" == "$action" ] ; then
 	field="`cat $input 2> /dev/null | head -n 1 | cut -f$4 | tr '\n\r' ' '`"
 	newname=$5
-	/data/users/david/anaconda3/bin/python $dir/ParseDb.py rename -d $input --outdir $PWD/outdir --outname output -f $field -k $newname
+	python3 $dir/ParseDb.py rename -d $input --outdir $PWD/outdir --outname output -f $field -k $newname
 	mv $PWD/outdir/output_parse-rename.tab $output
 elif [ "select" == "$action" ] ; then
 	field="`cat $input 2> /dev/null | head -n 1 | cut -f$4 | tr '\n\r' ' '`"
@@ -61,7 +61,7 @@
 	else
 		regex=""
 	fi
-	/data/users/david/anaconda3/bin/python $dir/ParseDb.py select -d $input --outdir $PWD/outdir --outname output -f $field -u $value --logic any $regex
+	python3 $dir/ParseDb.py select -d $input --outdir $PWD/outdir --outname output -f $field -u $value --logic any $regex
 	mv $PWD/outdir/output_parse-select.tab $output
 elif [ "sort" == "$action" ] ; then
 	field="`cat $input 2> /dev/null | head -n 1 | cut -f$4 | tr '\n\r' ' '`"
@@ -74,7 +74,7 @@
 	if [ "true" == "$desc" ] ; then
 		tmp="--descend $tmp"
 	fi	
-	/data/users/david/anaconda3/bin/python $dir/ParseDb.py sort -d $input --outdir $PWD/outdir --outname output -f $field $tmp
+	python3 $dir/ParseDb.py sort -d $input --outdir $PWD/outdir --outname output -f $field $tmp
 	mv $PWD/outdir/output_parse-sort.tab $output
 elif [ "update" == "$action" ] ; then
 	field="`cat $input 2> /dev/null | head -n 1 | cut -f$4 | tr '\n\r' ' '`"
@@ -86,7 +86,7 @@
 	else
 		regex=""
 	fi
-	/data/users/david/anaconda3/bin/python $dir/ParseDb.py update -d $input --outdir $PWD/outdir --outname output -f $field -u $value -t $replace $regex
+	python3 $dir/ParseDb.py update -d $input --outdir $PWD/outdir --outname output -f $field -u $value -t $replace $regex
 	mv $PWD/outdir/output_parse-update.tab $output
 fi