--- a/loadandplot.xml	Fri Jun 09 12:27:10 2017 -0400
+++ b/loadandplot.xml	Wed Jun 14 13:57:38 2017 -0400
@@ -23,68 +23,68 @@
 
   <command>
 <![CDATA[
-    Rscript $__tool_directory__/loadandplot.R outrdata="${outrdata}" outregions="${outregions}" outfeatures="${outfeatures}" outpdf="${outpdf}"
+    Rscript '$__tool_directory__/loadandplot.R' outrdata='${outrdata}' outregions='${outregions}' outfeatures='${outfeatures}' outpdf='${outpdf}'
 
       #set region_paths = '"\\|"'.join( [ str( $r ) for $r in $regions ] )
-      regionspaths="${region_paths}"
+      regionspaths='${region_paths}'
       #set region_galaxyids = '","'.join( [ str( $r.hid ) for $r in $regions ] )
-      regionsgalaxyids="c(${region_galaxyids})"
+      regionsgalaxyids='c(${region_galaxyids})'
       #set region_names = '"\\|"'.join( [ str( $r.name ) for $r in $regions ] )
-      regionsfilenames="${region_names}"
-      #set region_header = '"\\|"'.join( [ str( $rh.regionsheader ) for $rh in $regionsheaderrepeat ] )
+      regionsfilenames='${region_names}'
+      #set region_header = "${regionsheadersection.regionsheader}"
       #if $region_header != "":
-        regionsheaderfile="${region_header}"
+        regionsheaderfile='${region_header}'
       #end if
-
+      
       #set feature_paths = '"\\|"'.join( [ str( $f ) for $f in $features ] )
-      featurespaths="${feature_paths}"
+      featurespaths='${feature_paths}'
       #set feature_galaxyids = '","'.join( [ str( $f.hid ) for $f in $features ] )
-      featuresgalaxyids="c(${feature_galaxyids})"
+      featuresgalaxyids='c(${feature_galaxyids})'
       #set feature_names = '"\\|"'.join( [ str( $f.name ) for $f in $features ] )
-      featuresfilenames="${feature_names}"
-      #set feature_header = '"\\|"'.join( [ str( $fh.featuresheader ) for $fh in $featuresheaderrepeat ] )
+      featuresfilenames='${feature_names}'
+      #set feature_header = "${featuresheadersection.featuresheader}"
       #if $feature_header != "":
-        featuresheaderfile="${feature_header}"
+        featuresheaderfile='${feature_header}'
       #end if
 
-      smoothing="'${conditionaltype.smoothing}'"
-      start.are.0based="${zerobased}"
+      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}"
+          scale='${conditionaltype.locpolyconditionalscale.scalegrid}'
         #end if
-        bandwidth="${conditionaltype.locpolybandwidth}"
-        degree="${conditionaltype.locpolydegree}"
-        fill_gaps="${conditionaltype.fillgaps}"
+        bandwidth='${conditionaltype.locpolybandwidth}'
+        degree='${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}"
+          scale='${conditionaltype.kernelconditionalscale.scalegrid}'
         #end if
-        bandwidth="${conditionaltype.kernelbandwidth}"
-        fill_gaps="${conditionaltype.fillgaps}"
+        bandwidth='${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}"
+          scale='${conditionaltype.splinesconditionalscale.scalegrid}'
         #end if
-        degree="${conditionaltype.splinesdegree}"
-        dist_knots="${conditionaltype.splinesdistknots}"
-        fill_gaps="${conditionaltype.fillgaps}"
+        degree='${conditionaltype.splinesdegree}'
+        dist_knots='${conditionaltype.splinesdistknots}'
+        fill_gaps='${conditionaltype.fillgaps}'
       #end if
 
-      average="${plotres.average}"
-      size="${plotres.size}"
-      plottype="'${plotres.conditionalplottype.plottype}'"
+      average='${plotres.average}'
+      size='${plotres.size}'
+      plottype='${plotres.conditionalplottype.plottype}'
       #if $plotres.conditionalplottype.plottype == 'boxplot':
         #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},${probs})"
+          probs='c(${plotres.conditionalplottype.probabilitiessection.prob0},${plotres.conditionalplottype.probabilitiessection.prob1},${plotres.conditionalplottype.probabilitiessection.prob2},${probs})'
         #else:
-          probs="c(${plotres.conditionalplottype.probabilitiessection.prob0},${plotres.conditionalplottype.probabilitiessection.prob1},${plotres.conditionalplottype.probabilitiessection.prob2})"
+          probs='c(${plotres.conditionalplottype.probabilitiessection.prob0},${plotres.conditionalplottype.probabilitiessection.prob1},${plotres.conditionalplottype.probabilitiessection.prob2})'
         #end if
       #end if
 
@@ -99,15 +99,15 @@
   <inputs>
     <!-- regions -->
     <param format="tabular" name="regions" type="data" label="Select region files" multiple="true" help="" />
-    <repeat name="regionsheaderrepeat" title="Header file for regions (optional)" min="0" max="1" help="Tabular file. Column 1: names of the region files; Column 2: unique identifiers of the region datasets (spaces and special characters are not allowed); Column 3: name of the region datasets to be used in the output.">
-      <param format="tabular" name="regionsheader" type="data" label="Select header file" />
-    </repeat>
+    <section name="regionsheadersection" title="Insert header file for regions (optional)" expanded="false" help="Tabular file. Column 1: names of the region files; Column 2: unique identifiers of the region datasets (spaces and special characters are not allowed); Column 3: name of the region datasets to be used in the output.">
+      <param format="tabular" name="regionsheader" type="data" label="Select header file" optional="true" />
+    </section>
 
     <!-- features -->
     <param format="tabular" name="features" type="data" label="Select feature files" multiple="true" help="" />
-    <repeat name="featuresheaderrepeat" title="Header file for features (optional)" min="0" max="1" help="Tabular file. Column 1: names of the feature files; Column 2: unique identifiers of the features (spaces and special characters are not allowed); Column 3: name of the features to be used in the output.">
-      <param format="tabular" name="featuresheader" type="data" label="Select header file" />
-    </repeat>
+    <section name="featuresheadersection" title="Insert header file for features (optional)" expanded="false" help="Tabular file. Column 1: names of the feature files; Column 2: unique identifiers of the features (spaces and special characters are not allowed); Column 3: name of the features to be used in the output.">
+      <param format="tabular" name="featuresheader" type="data" label="Select header file" optional="true" />
+    </section>
 
     <!-- zero-base one-base -->
     <param name="zerobased" type="select" label="Start positions are:" multiple="false" help="">
@@ -330,28 +330,6 @@
 .. _ETn_data: https://usegalaxy.org/u/fabio-cumbo/h/iwtomics-etn-example
   ]]></help>
 
-  <citations>
-    <citation type="bibtex">
-      @ARTICLE{
-               iwt-functional-data,
-               author = {Pini, Alessia and Vantini, Simone},
-               title = {Interval-Wise Testing for functional data},
-               journal = {Journal of Nonparametric Statistics},
-               year = {2017},
-               volume = {29},
-               number = {2},
-               pages = {407-424}
-      }
-    </citation>
-    <citation type="bibtex">
-      @MANUAL{
-               iwtomics,
-               author = {Cremona, Marzia A and Pini, Alessia and Chiaromonte, Francesca and Vantini, Simone},
-               title = {IWTomics: Interval-Wise Testing for Omics Data},
-               note = {R package version 1.0.0},
-               year = {2017}
-      }
-    </citation>
-  </citations>
+  <expand macro="citations" />
 
 </tool>