--- a/GRsetFromGEO/GRsetFromGEO.xml	Mon Aug 21 06:28:18 2017 -0400
+++ b/GRsetFromGEO/GRsetFromGEO.xml	Wed Sep 06 06:02:44 2017 -0400
@@ -1,25 +1,27 @@
 <tool id="getGRset" name="GRsetFromGEO">
-  <description>downloads data from GEO</description>
-  <requirements>
-<requirement type="package" version="1.20.0">bioconductor-minfi</requirement>
-<requirement type="package" version="0.6.0">bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19</requirement>
-  </requirements>
-  <stdio>
-  <exit_code range="1:" />
-  </stdio>
-  <command>Rscript $__tool_directory__/GRsetFromGEO.R "$input" "$output"</command>
-  <inputs>
-    <param format="text" name="input" type="text" value="" label="Enter GSE ID." help="e.g. 'GSE51547'"/>
-  </inputs>
-  <outputs>
-    <data format="rdata" name="output" label="output.rdata" />
-  </outputs>
-  <help>
+    <description>downloads data from GEO</description>
+    <requirements>
+        <requirement type="package" version="1.20.0">bioconductor-minfi</requirement>
+        <requirement type="package" version="0.6.0">bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19</requirement>
+    </requirements>
+    <command detect_errors="aggressive">
+        Rscript '$__tool_directory__/GRsetFromGEO.R' '$input' '$output'
+    </command>
+    <inputs>
+        <param format="text" name="input" type="text" value="" label="Enter GSE ID." help="e.g. 'GSE51547'"/>
+    </inputs>
+    <outputs>
+        <data format="rdata" name="output" label="output.rdata" />
+    </outputs>
+    <help>
     **What it does**
+    
     This R-based tool downloads data from GEO using getGEO from the GEOquery package and then returns a GenomicRatioSet object
+    
     **Input**
     The GSE ID of the dataset to be downloaded from GEO "e.g. 'GSE51547'"
+    
     **Output**
     GenomicRatioSet object
-  </help>
+    </help>
 </tool>