Mercurial > repos > testtool > get_gr_set

changeset 4:86777f72f33c draft

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Uploaded
author testtool
date Sun, 11 Jun 2017 06:38:17 -0400
parents 6521cdfa99a8
children 7511130b5068
files getGRsetFromGEO/getGRsetFromGEO.xml
diffstat 1 files changed, 39 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/getGRsetFromGEO/getGRsetFromGEO.xml	Sun Jun 11 06:38:17 2017 -0400
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+<?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>