diff GRsetFromGEO/GRsetFromGEO.xml @ 5:7511130b5068 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/GRsetFromGEO/GRsetFromGEO.xml	Sun Jun 11 07:49:41 2017 -0400
@@ -0,0 +1,39 @@
+<?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"/>
+        </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>
+</tool>