# HG changeset patch
# User testtool
# Date 1515692909 18000
# Node ID 2382697aad099159ad1a01ddeb8151386782750d
# Parent  dc0d9276a8f1e0bfc37ee8a5ff1f5576ae39e3fc
Uploaded

diff -r dc0d9276a8f1 -r 2382697aad09 GRsetFromGEO/._GRsetFromGEO.xml
Binary file GRsetFromGEO/._GRsetFromGEO.xml has changed
diff -r dc0d9276a8f1 -r 2382697aad09 GRsetFromGEO/._~$setFromGEO.xml
Binary file GRsetFromGEO/._~$setFromGEO.xml has changed
diff -r dc0d9276a8f1 -r 2382697aad09 GRsetFromGEO/GRsetFromGEO.R
--- a/GRsetFromGEO/GRsetFromGEO.R	Wed Sep 06 06:02:44 2017 -0400
+++ b/GRsetFromGEO/GRsetFromGEO.R	Thu Jan 11 12:48:29 2018 -0500
@@ -1,4 +1,8 @@
 require(minfi, quietly = TRUE)
+require(IlluminaHumanMethylation450kanno.ilmn12.hg19, quietly = TRUE)
+
+options('GEOquery.inmemory.gpl'=TRUE)
+options('download.file.method.GEOquery' = 'libcurl')
 
 options(warn = -1)
 
@@ -8,6 +12,5 @@
 
 GRset <- getGenomicRatioSetFromGEO(input)
 
-save(GRset,file = output)
+save(GRset, file = output)
 
-
diff -r dc0d9276a8f1 -r 2382697aad09 GRsetFromGEO/GRsetFromGEO.xml
--- a/GRsetFromGEO/GRsetFromGEO.xml	Wed Sep 06 06:02:44 2017 -0400
+++ b/GRsetFromGEO/GRsetFromGEO.xml	Thu Jan 11 12:48:29 2018 -0500
@@ -1,4 +1,4 @@
-<tool id="getGRset" name="GRsetFromGEO">
+<tool id="getGRset" name="GRsetFromGEO" version="1.0.0">
     <description>downloads data from GEO</description>
     <requirements>
         <requirement type="package" version="1.20.0">bioconductor-minfi</requirement>
@@ -8,20 +8,30 @@
         Rscript '$__tool_directory__/GRsetFromGEO.R' '$input' '$output'
     </command>
     <inputs>
-        <param format="text" name="input" type="text" value="" label="Enter GSE ID." help="e.g. 'GSE51547'"/>
+        <param format="text" name="input" type="text" value="" label="Enter GSE ID." help="e.g. 'GSE42752'"/>
     </inputs>
     <outputs>
         <data format="rdata" name="output" label="output.rdata" />
     </outputs>
-    <help>
-    **What it does**
-    
-    This R-based tool downloads data from GEO using getGEO from the GEOquery package and then returns a GenomicRatioSet object
-    
-    **Input**
-    The GSE ID of the dataset to be downloaded from GEO "e.g. 'GSE51547'"
-    
-    **Output**
-    GenomicRatioSet object
-    </help>
+    <tests>
+       <test>
+           <param name="input" value="GSE42752"/>
+           <output name="output" file="out.rdata"/>
+       </test>
+   </tests>
+   <help>
+   **What it does**
+
+   This R-based tool downloads data from GEO using getGEO from the GEOquery package and then returns a GenomicRatioSet object
+
+   **Input**
+   The GSE ID of the dataset to be downloaded from GEO "e.g. 'GSE51547'"
+
+   **Output**
+   GenomicRatioSet object
+   </help>
+   <citations>
+   <citation type="doi">10.1093/bioinformatics/btm254</citation>
+   <citation type="doi">10.1093/bioinformatics/btu049</citation>
+   </citations>
 </tool>
diff -r dc0d9276a8f1 -r 2382697aad09 GRsetFromGEO/test-data/._.DS_Store
Binary file GRsetFromGEO/test-data/._.DS_Store has changed
diff -r dc0d9276a8f1 -r 2382697aad09 GRsetFromGEO/test-data/out.RData
Binary file GRsetFromGEO/test-data/out.RData has changed
diff -r dc0d9276a8f1 -r 2382697aad09 GRsetFromGEO/test-data/out.rdata
Binary file GRsetFromGEO/test-data/out.rdata has changed
diff -r dc0d9276a8f1 -r 2382697aad09 GRsetFromGEO/~$setFromGEO.xml
Binary file GRsetFromGEO/~$setFromGEO.xml has changed