# HG changeset patch
# User testtool
# Date 1497176497 14400
# Node ID 457c1fc71f642a8923abd2478fdfeb20b883e78c

Uploaded

diff -r 000000000000 -r 457c1fc71f64 getGRsetFromGEO/.Rapp.history
diff -r 000000000000 -r 457c1fc71f64 getGRsetFromGEO/.Rhistory
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/getGRsetFromGEO/.Rhistory	Sun Jun 11 06:21:37 2017 -0400
@@ -0,0 +1,16 @@
+require("minfi", quietly = TRUE)
+?require
+require("minfi", quietly = TRUE)
+minfi
+as.data.frame(GRset)
+GRset <- getGenomicRatioSetFromGEO(GSE)
+getGenomicRatioSetFromGEO
+require("minfi", quietly = TRUE)
+options(warn = -1)
+options("download.file.method"="wget")
+args <- commandArgs(trailingOnly = TRUE)
+GSE = args[1]
+output = args[2]
+GRset <- getGenomicRatioSetFromGEO(GSE)
+save(GRset,file = output)
+sessionInfo()
diff -r 000000000000 -r 457c1fc71f64 getGRsetFromGEO/._.DS_Store
Binary file getGRsetFromGEO/._.DS_Store has changed
diff -r 000000000000 -r 457c1fc71f64 getGRsetFromGEO/getGRsetFromGEO.R
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/getGRsetFromGEO/getGRsetFromGEO.R	Sun Jun 11 06:21:37 2017 -0400
@@ -0,0 +1,12 @@
+require("minfi", quietly = TRUE)
+
+options(warn = -1)
+options("download.file.method"="wget")
+
+args <- commandArgs(trailingOnly = TRUE)
+GSE = args[1] 
+output = args[2] 
+
+GRset <- getGenomicRatioSetFromGEO(GSE)
+
+save(GRset,file = output)
diff -r 000000000000 -r 457c1fc71f64 getGRsetFromGEO/getGRsetFromGEO.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/getGRsetFromGEO/getGRsetFromGEO.xml	Sun Jun 11 06:21:37 2017 -0400
@@ -0,0 +1,39 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<tool id="getGRsetFromGEO" name="getGRsetFromGEO" version="1.18.4">
+  <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>
diff -r 000000000000 -r 457c1fc71f64 getGRsetFromGEO/test-data/._.DS_Store
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diff -r 000000000000 -r 457c1fc71f64 getGRsetFromGEO/test-data/out.RData
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