--- a/plotwithscale.xml	Fri Jun 09 12:27:10 2017 -0400
+++ b/plotwithscale.xml	Wed Jun 14 13:57:38 2017 -0400
@@ -17,38 +17,38 @@
 
   <command>
 <![CDATA[
-    Rscript $__tool_directory__/plotwithscale.R adjustedpvalue="${adjustedpvalue}" iwtomicsrespdf="${iwtomicsrespdf}" iwtomicssumpdf="${iwtomicssumpdf}"
-      iwtomicsrdata="${rdata}"
-      iwtomicstests="${testids}"
-      iwtomicsselectedfeatures="${featureids}"
+    Rscript '$__tool_directory__/plotwithscale.R' adjustedpvalue='${adjustedpvalue}' iwtomicsrespdf='${iwtomicsrespdf}' iwtomicssumpdf='${iwtomicssumpdf}'
+      iwtomicsrdata='${rdata}'
+      iwtomicstests='${testids}'
+      iwtomicsselectedfeatures='${featureids}'
 
       #set test_subset = '"\\|"'.join( [ str( $e.test ) for $e in $scalesection.thresholdontestscale ] )
-      test_subset="${test_subset}"
+      test_subset='${test_subset}'
       #set feature_subset = '"\\|"'.join( [ str( $e.feature ) for $e in $scalesection.thresholdontestscale ] )
-      feature_subset="${feature_subset}"
+      feature_subset='${feature_subset}'
       #set scale_subset = '","'.join( [ str( $e.scale ) for $e in $scalesection.thresholdontestscale ] )
-      scale_subset="c(${scale_subset})"
+      scale_subset='c(${scale_subset})'
 
-      testalpha="${plotres.alpha}"
-      average="${plotres.average}"
-      size="${plotres.size}"
-      plottype="'${plotres.conditionalplottype.plottype}'"
+      testalpha='${plotres.alpha}'
+      average='${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
 
-      groupby="'${plotsum.conditionalgroupby.groupby}'"
+      groupby='${plotsum.conditionalgroupby.groupby}'
       #if $plotsum.conditionalgroupby.groupby == "test":
-        summaryalpha="${plotsum.conditionalgroupby.testalphaplot}"
-        only_significant="${plotsum.conditionalgroupby.testonlysig}"
+        summaryalpha='${plotsum.conditionalgroupby.testalphaplot}'
+        only_significant='${plotsum.conditionalgroupby.testonlysig}'
       #elif $plotsum.conditionalgroupby.groupby == "feature":
-        summaryalpha="${plotsum.conditionalgroupby.featurealphaplot}"
-        only_significant="${plotsum.conditionalgroupby.featureonlysig}"
+        summaryalpha='${plotsum.conditionalgroupby.featurealphaplot}'
+        only_significant='${plotsum.conditionalgroupby.featureonlysig}'
       #end if
 
       >& /dev/null
@@ -201,28 +201,6 @@
 .. _vignette: https://bioconductor.org/packages/release/bioc/vignettes/IWTomics/inst/doc/IWTomics.pdf
   ]]></help>
 
-  <citations>
-    <citation type="bibtex">
-      @ARTICLE{
-               iwt-functional-data,
-               author = {A Pini and S. Vantini},
-               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>