# HG changeset patch
# User testtool
# Date 1499696647 14400
# Node ID 4f157ee63207cfe3fdbe3819d5bb500fb5cb3afd
# Parent  5d796e9a96aec0e01178a3067dd012f5085f09dc
Uploaded

diff -r 5d796e9a96ae -r 4f157ee63207 GRsetFromGEO/GRsetFromGEO.xml
--- a/GRsetFromGEO/GRsetFromGEO.xml	Mon Jul 10 09:09:09 2017 -0400
+++ b/GRsetFromGEO/GRsetFromGEO.xml	Mon Jul 10 10:24:07 2017 -0400
@@ -1,39 +1,26 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<tool id="GetGEO" name="GRsetFromGEO" version="1.16.2">
-<requirements>
-<requirement type="package" version="1.20.0">bioconductor-minfi</requirement>
-</requirements>
-<stdio>
-<exit_code range="1:" />
-</stdio>
+<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="0.2.1">bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19</requirement>
+  </requirements>
+  <stdio>
+  <exit_code range="1:" />
+  </stdio>
   <command>Rscript $__tool_directory__/GRsetFromGEO.R $input output.RData</command>
   <inputs>
-     <param 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. 'GSE51547'"/>
   </inputs>
   <outputs>
-    <data format="RDdata" name="output" label="GRsetFromGEO.RData"/>
+    <data format="RDdata" name="output" label="output.RData" />
   </outputs>
-  <tests>
-    <test>
-      <param name="test">
-      <element name="test-data">
-          <collection type="data">
-                <element name="input" value="GSE51547"/>
-          </collection>
-        </element>
-        </param>
-        <output type="data" format="RData"  name="output" label="test-data/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
+    **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/btu049</citation>
-  </citations>
 </tool>
+Rscript $__tool_directory__/GRsetFromGEO.R "$input" "$output"