--- a/loadandplot.xml	Wed Jun 14 13:58:04 2017 -0400
+++ b/loadandplot.xml	Wed Jun 14 15:20:32 2017 -0400
@@ -25,34 +25,34 @@
 <![CDATA[
     Rscript '$__tool_directory__/loadandplot.R' outrdata='${outrdata}' outregions='${outregions}' outfeatures='${outfeatures}' outpdf='${outpdf}'
 
-      #set region_paths = '"\\|"'.join( [ str( $r ) for $r in $regions ] )
+      #set region_paths = '|'.join( [ str( $r ) for $r in $regions ] )
       regionspaths='${region_paths}'
-      #set region_galaxyids = '","'.join( [ str( $r.hid ) for $r in $regions ] )
+      #set region_galaxyids = ','.join( [ str( $r.hid ) for $r in $regions ] )
       regionsgalaxyids='c(${region_galaxyids})'
-      #set region_names = '"\\|"'.join( [ str( $r.name ) for $r in $regions ] )
+      #set region_names = '|'.join( [ str( $r.name ) for $r in $regions ] )
       regionsfilenames='${region_names}'
-      #set region_header = "${regionsheadersection.regionsheader}"
+      #set region_header = $regionsheadersection.regionsheader
       #if $region_header != "":
         regionsheaderfile='${region_header}'
       #end if
       
-      #set feature_paths = '"\\|"'.join( [ str( $f ) for $f in $features ] )
+      #set feature_paths = '|'.join( [ str( $f ) for $f in $features ] )
       featurespaths='${feature_paths}'
-      #set feature_galaxyids = '","'.join( [ str( $f.hid ) for $f in $features ] )
+      #set feature_galaxyids = ','.join( [ str( $f.hid ) for $f in $features ] )
       featuresgalaxyids='c(${feature_galaxyids})'
-      #set feature_names = '"\\|"'.join( [ str( $f.name ) for $f in $features ] )
+      #set feature_names = '|'.join( [ str( $f.name ) for $f in $features ] )
       featuresfilenames='${feature_names}'
-      #set feature_header = "${featuresheadersection.featuresheader}"
+      #set feature_header = $featuresheadersection.featuresheader
       #if $feature_header != "":
         featuresheaderfile='${feature_header}'
       #end if
 
-      smoothing='${conditionaltype.smoothing}'
+      smoothing="'${conditionaltype.smoothing}'"
       start.are.0based='${zerobased}'
       #if $conditionaltype.smoothing == 'no':
-        alignment='${conditionaltype.alignment}'
+        alignment="'${conditionaltype.alignment}'"
       #elif $conditionaltype.smoothing == 'locpoly':
-        alignment='${conditionaltype.locpolyconditionalscale.alignment}'
+        alignment="'${conditionaltype.locpolyconditionalscale.alignment}'"
         #if $conditionaltype.locpolyconditionalscale.alignment == 'scale':
           scale='${conditionaltype.locpolyconditionalscale.scalegrid}'
         #end if
@@ -60,14 +60,14 @@
         degree='${conditionaltype.locpolydegree}'
         fill_gaps='${conditionaltype.fillgaps}'
       #elif $conditionaltype.smoothing == 'kernel':
-        alignment='${conditionaltype.kernelconditionalscale.alignment}'
+        alignment="'${conditionaltype.kernelconditionalscale.alignment}'"
         #if $conditionaltype.kernelconditionalscale.alignment == 'scale':
           scale='${conditionaltype.kernelconditionalscale.scalegrid}'
         #end if
         bandwidth='${conditionaltype.kernelbandwidth}'
         fill_gaps='${conditionaltype.fillgaps}'
       #elif $conditionaltype.smoothing == 'splines':
-        alignment='${conditionaltype.splinesconditionalscale.alignment}'
+        alignment="'${conditionaltype.splinesconditionalscale.alignment}'"
         #if $conditionaltype.splinesconditionalscale.alignment == 'scale':
           scale='${conditionaltype.splinesconditionalscale.scalegrid}'
         #end if
@@ -78,9 +78,9 @@
 
       average='${plotres.average}'
       size='${plotres.size}'
-      plottype='${plotres.conditionalplottype.plottype}'
+      plottype="'${plotres.conditionalplottype.plottype}'"
       #if $plotres.conditionalplottype.plottype == 'boxplot':
-        #set probs = '","'.join( [ str( $p.prob ) for $p in $plotres.conditionalplottype.probabilitiessection.probabilities ] )
+        #set probs = ','.join( [ str( $p.prob ) for $p in $plotres.conditionalplottype.probabilitiessection.probabilities ] )
         #if $probs != "":
           probs='c(${plotres.conditionalplottype.probabilitiessection.prob0},${plotres.conditionalplottype.probabilitiessection.prob1},${plotres.conditionalplottype.probabilitiessection.prob2},${probs})'
         #else: