# HG changeset patch
# User testtool
# Date 1492100373 14400
# Node ID cc4b808cb2eaec1e61f9a8a6af0319f2b2a621ff
# Parent  ceced09589d9d3292c6eaa1003391952bca231a8
Uploaded

diff -r ceced09589d9 -r cc4b808cb2ea GRsetFromGEO/GRsetFromGEO.xml
--- a/GRsetFromGEO/GRsetFromGEO.xml	Thu Apr 13 12:06:07 2017 -0400
+++ b/GRsetFromGEO/GRsetFromGEO.xml	Thu Apr 13 12:19:33 2017 -0400
@@ -1,6 +1,6 @@
 <tool id="GRset" name="GRsetFromGEO" version="1.16.2">
   <requirements>
-  <requirement type="R-module" version="1.15.7">minfi</requirement>
+   <requirement name="package_r_3_2_1" type="package" version="3.2.1">R</requirement>
 </requirements>
 <stdio>
    <exit_code range="1:" />
@@ -10,7 +10,7 @@
     <param name="GSE" type="text" value="" label="Enter GSE ID." help="e.g. 'GSE51547'"/>
   </inputs>
   <outputs>
-    <data  ftype="RData" name="output" label="GenomicRatioSet.RData"/>
+    <data type="galaxy.datatypes.binary:RData" name="output" label="GenomicRatioSet.RData"/>
   </outputs>
   <tests>
     <test>
@@ -21,13 +21,13 @@
           </collection>
         </element>
         </param>
-        <output   ftype="RData" name="output" label="test-data/GenomicRatioSet.RData"/>
+        <output  type="galaxy.datatypes.binary:RData" name="output" label="test-data/GenomicRatioSet.RData"/>
         </test>
     </tests>
   <help>
-Reading Illumina methylation array data from GEO
+Reading Illumina methylation array data from GEO.
 </help>
 <citations>
-xxx
+Aryee, Martin J., et al. "Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays." Bioinformatics 30.10 (2014): 1363-1369.
 </citations>
 </tool>
diff -r ceced09589d9 -r cc4b808cb2ea GRsetFromGEO/tool_dependencies.xml
--- a/GRsetFromGEO/tool_dependencies.xml	Thu Apr 13 12:06:07 2017 -0400
+++ b/GRsetFromGEO/tool_dependencies.xml	Thu Apr 13 12:19:33 2017 -0400
@@ -1,6 +1,5 @@
-<?xml version="1.0"?>
+<?xml version='1.0' encoding='utf-8' ?>
 <tool_dependency>
-  <install version="1.0">
     <actions>
                 <action type="setup_r_environment">
                   <repository changeset_revision="d0bf97420fb5" name="package_r_3_2_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
@@ -272,5 +271,4 @@
                       </package>
                   </action>
               </actions>
-              </install>
-            </tool_dependency>
+            </tool_dependency>
\ No newline at end of file