Mercurial > repos > testtool > get_gr_set

diff GRsetFromGEO.xml @ 25:b2a0cc48c838 draft

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author testtool
date Mon, 10 Jul 2017 08:58:24 -0400
parents 1bdfe0d48de8
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/GRsetFromGEO.xml	Mon Jul 10 08:58:24 2017 -0400
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+<tool id="getGRset" name="GRsetFromGEO">
+  <description>downloads data from GEO</description>
+  <command>Rscript $__tool_directory__/GRsetFromGEO.R $input output.RData</command>
+  <inputs>
+    <param format="text" name="input" type="text" value="" label="Enter GSE ID." help="e.g. 'GSE51547'"/>
+  </inputs>
+  <outputs>
+    <data format="RDdata" name="output" label="output.RData" />
+  </outputs>
+  <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>
+</tool>