# HG changeset patch
# User testtool
# Date 1497181781 14400
# Node ID 7511130b5068749c60d1d0981becbba942992875
# Parent  86777f72f33c543c4276b1129f33ee269ea7ff03
Uploaded

diff -r 86777f72f33c -r 7511130b5068 GRsetFromGEO/.Rapp.history
diff -r 86777f72f33c -r 7511130b5068 GRsetFromGEO/.Rhistory
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/GRsetFromGEO/.Rhistory	Sun Jun 11 07:49:41 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 86777f72f33c -r 7511130b5068 GRsetFromGEO/GRsetFromGEO.R
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/GRsetFromGEO/GRsetFromGEO.R	Sun Jun 11 07:49:41 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 86777f72f33c -r 7511130b5068 GRsetFromGEO/GRsetFromGEO.xml
--- /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>
diff -r 86777f72f33c -r 7511130b5068 GRsetFromGEO/test-data/out.RData
Binary file GRsetFromGEO/test-data/out.RData has changed
diff -r 86777f72f33c -r 7511130b5068 getGRsetFromGEO/.Rapp.history
diff -r 86777f72f33c -r 7511130b5068 getGRsetFromGEO/.Rhistory
--- a/getGRsetFromGEO/.Rhistory	Sun Jun 11 06:38:17 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,16 +0,0 @@
-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 86777f72f33c -r 7511130b5068 getGRsetFromGEO/._.DS_Store
Binary file getGRsetFromGEO/._.DS_Store has changed
diff -r 86777f72f33c -r 7511130b5068 getGRsetFromGEO/getGRsetFromGEO.R
--- a/getGRsetFromGEO/getGRsetFromGEO.R	Sun Jun 11 06:38:17 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,12 +0,0 @@
-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 86777f72f33c -r 7511130b5068 getGRsetFromGEO/getGRsetFromGEO.xml
--- a/getGRsetFromGEO/getGRsetFromGEO.xml	Sun Jun 11 06:38:17 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,39 +0,0 @@
-<?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 $__tool_directory__/getGRsetFromGEO.R "$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="getGRsetFromGEO.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 86777f72f33c -r 7511130b5068 getGRsetFromGEO/test-data/._.DS_Store
Binary file getGRsetFromGEO/test-data/._.DS_Store has changed
diff -r 86777f72f33c -r 7511130b5068 getGRsetFromGEO/test-data/out.RData
Binary file getGRsetFromGEO/test-data/out.RData has changed