--- a/loadandplot.xml	Wed Jun 14 15:20:56 2017 -0400
+++ b/loadandplot.xml	Mon Jun 19 12:08:59 2017 -0400
@@ -4,24 +4,8 @@
     <import>macros.xml</import>
   </macros>
   <expand macro="requirements" />
-  <stdio>
-    <exit_code range="255" level="fatal" description="Missing IWTomics package. Please be sure to have it installed before using this tool." />
-    <exit_code range="10" level="fatal" description="An error has occurred reading the header file for regions. Please try again." />
-    <exit_code range="11" level="fatal" description="Not all region files are present in the first column of header file for regions." />
-    <exit_code range="20" level="fatal" description="An error has occurred reading the header file for features. Please try again." />
-    <exit_code range="21" level="fatal" description="Not all feature files are present in the first column of header file for features." />
-    <exit_code range="30" level="fatal" description="An error has occurred reading the data. Please try again." />
-    <exit_code range="31" level="fatal" description="Not enough columns in input file." />
-    <exit_code range="32" level="fatal" description="Duplicated regions in region file." />
-    <exit_code range="33" level="fatal" description="Duplicated windows in feature file." />
-    <exit_code range="34" level="fatal" description="Overlapping windows in feature file." />
-    <exit_code range="35" level="fatal" description="Windows in feature files do not cover all regions in region files." />
-    <exit_code range="36" level="fatal" description="All windows in a feature file must have the same size." />
-    <exit_code range="40" level="fatal" description="An error has occurred smoothing the data. Please try again." />
-    <regex match="Error" source="both" level="fatal" description="An error has occurred. Please try again." />
-  </stdio>
 
-  <command>
+  <command detect_errors="exit_code">
 <![CDATA[
     Rscript '$__tool_directory__/loadandplot.R' outrdata='${outrdata}' outregions='${outregions}' outfeatures='${outfeatures}' outpdf='${outpdf}'
 
@@ -86,14 +70,8 @@
         #else:
           probs='c(${plotres.conditionalplottype.probabilitiessection.prob0},${plotres.conditionalplottype.probabilitiessection.prob1},${plotres.conditionalplottype.probabilitiessection.prob2})'
         #end if
-      #end if
-
-      >& /dev/null
+      #end if      
 ]]>
-    <!--
-    to print the stack add the following line at the end of the command and enable the corresponding entry in output
-    2> "${stackerr}"
-    -->
   </command>
 
   <inputs>
@@ -225,7 +203,6 @@
   </inputs>
 
   <outputs>
-    <!--<data format="txt" name="stackerr" label="iwtomics.loadandplot.stackerr.txt" from_work_dir="iwtomics.loadandplot.stackerr.txt" />-->
     <data format="rdata" name="outrdata" label="${tool.name} on ${on_string}: IWTomicsData Object" from_work_dir="iwtomics.loadandplot.RData" />
     <data format="tabular" name="outregions" label="${tool.name} on ${on_string}: Region Dataset IDs" from_work_dir="iwtomics.loadandplot.regions.txt" />
     <data format="tabular" name="outfeatures" label="${tool.name} on ${on_string}: Feature IDs" from_work_dir="iwtomics.loadandplot.features.txt" />