Mercurial > repos > testtool > get_gr_set

changeset 18:25490621d43e draft

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Uploaded
author testtool
date Mon, 03 Jul 2017 07:13:38 -0400
parents 3431c6054674
children 0a619d0e45fd
files GRsetFromGEO.xml
diffstat 1 files changed, 39 insertions(+), 0 deletions(-) [+]
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+++ b/GRsetFromGEO.xml	Mon Jul 03 07:13:38 2017 -0400
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+<?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 $__tool_directory__/GRsetFromGEO.R "$input" "$output" </command>
+  <inputs>
+     <param name="input" 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="input" 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>