# HG changeset patch
# User testtool
# Date 1498737853 14400
# Node ID 6c3be09de899cf296af5615f58590becfb3302fc
# Parent  c3b28b232e6432e3dee8efc8587bbc4a9a628c7b
Uploaded

diff -r c3b28b232e64 -r 6c3be09de899 GRsetFromGEO/GRsetFromGEO.xml
--- a/GRsetFromGEO/GRsetFromGEO.xml	Wed Jun 14 12:23:00 2017 -0400
+++ b/GRsetFromGEO/GRsetFromGEO.xml	Thu Jun 29 08:04:13 2017 -0400
@@ -1,39 +1,32 @@
-<?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>
-  <command> Rscript $__tool_directory__/GRsetFromGEO.R "$GSE" "$output" </command>
-  <inputs>
-     <param name="GSE" type="text" value="" label="Enter GSE ID." help="e.g. 'GSE51547'"/>
-  </inputs>
-  <outputs>
-    <data format="RDdata" name="output" label="GRsetFromGEO.RData"/>
-  </outputs>
-  <tests>
-    <test>
-      <param name="test">
-      <element name="test-data">
-          <collection type="data">
-                <element name="GSE" value="GSE51547"/>
-          </collection>
-        </element>
-        </param>
-        <output type="data" format="RData"  name="output" label="test-data/out.RData"/>
+<tool id="GetGEO" name="GRsetFromGEO" version="0.1.0">
+    <requirements>
+        <requirement type="package" version="1.20.0">bioconductor-minfi</requirement>
+    </requirements>
+    <stdio>
+        <exit_code range="1:" />
+    </stdio>
+    <command><![CDATA[
+      Rscript $__tool_directory__/GRsetFromGEO.R -a "$input" > "$output"
+    ]]></command>
+    <inputs>
+        <param type="text" name="input" value="" label="Enter GSE ID." help="e.g. 'GSE51547'"/>
+    </inputs>
+    <outputs>
+        <data name="output" format="RDdata" label="GRsetFromGEO.RData"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="GSE51547"/>
+            <output name="output" file="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
-  </help>
-  <citations>
-<citation type="doi">10.1093/bioinformatics/btu049</citation>
-  </citations>
+    <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/btu049</citation>
+    </citations>
 </tool>