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Imported from capsule None
author sblanck
date Fri, 09 Sep 2016 04:23:04 -0400
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/GEOQuery.xml	Fri Sep 09 04:23:04 2016 -0400
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+<tool id="GEOQuery" name="GEOQuery">
+	<description>GEOQuery wrapper</description>
+	<requirements>
+	  <container type="docker">sblanck/smat</container>
+	</requirements>
+	<command>
+		/galaxy-tools/stderr_wrapper.py Rscript 
+		/galaxy-tools/transcriptomics/GEOquery/GEOQuery.R 
+		$GEOQueryID 
+		$GEOQueryData 
+		$GEOQueryRData 
+		$conditions
+		$transformation
+	</command>
+
+	<inputs>
+		<param name="GEOQueryID" type="text" size="12" optional="false" label="GEOQuery ID" help="">
+			<validator type="empty_field"/>
+		</param>
+	<param name="transformation" type="select" label="log2 transformation">
+			<option value="auto">auto</option>
+            <option value="yes">yes</option>
+            <option value="no">no</option>
+        </param>
+	</inputs>
+
+	<outputs>
+		<data format="tabular" name="GEOQueryData" label="GEOQuery Data of ${GEOQueryID}"/>
+		<data format="cond" name="conditions" label="conditions of ${GEOQueryID}"/>
+        <data format="rdata" name="GEOQueryRData" label="GEOQuery RData of ${GEOQueryID}"/>		
+	</outputs>
+<help>
+**What it does**     	
+
+This tool fetches microarray data directly from GEO database, based on the GEOQuery R package. Given a GSE accession ID, it returns an Rdata object containing the data and a text file (.cond file) summarizing the conditions of the experiment. 
+The .cond file is a text file containing one line per sample in the experiment. Each line is made of 3 columns:
+
+	- Sample ID 
+	- Condition of the biological sample
+	- Description of the biological sample
+
+**Example** of .cond file      	
+::
+
+ Sample ID 	Condition			Description
+ GSM80460	series of 16 tumors	GSM80460 OSCE-2T SERIES OF 16 TUMORS
+ GSM80461	series of 16 tumors	GSM80461 OSCE-4T Series of 16 Tumors
+ GSM80462	series of 16 tumors	GSM80462 OSCE-6T Series of 16 Tumors
+ GSM80476	series of 4 normals	GSM80476 OSCE-2N Series of 4 Normals
+ GSM80477	series of 4 normals	GSM80477 OSCE-9N Series of 4 Normals
+    
+**Results**
+	
+- Rdata object containing data for further analysis
+- Condition (.cond) file summarizing conditions of the experiment
+- Tabular (.txt) file containing expression data for each sample
+  		
+
+</help>
+
+
+</tool>