diff AffyQCnormalization.xml @ 2:93451f832736 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/AffyQCnormalization.xml	Tue Mar 21 10:28:47 2017 -0400
@@ -0,0 +1,62 @@
+<tool id="QCnormalization" name="QCnormalization" version="0.1.0">
+	<description>Quality control and normalization of affymetrix expression data</description>
+	<requirements>
+	  <!--container type="docker">sblanck/smat</container-->
+	  <requirement type="package" version="0.1.0">r-smagexp</requirement>
+	</requirements>
+	<command interpreter="python">
+		<![CDATA[
+		stderr_wrapper.py Rscript 
+		${__tool_directory__}/AffyQCnormalization.R
+		   	#for $input in $inputs
+                "${input}"
+			    "${input.name}"
+     		#end for
+			"${normalization}"
+			$result_export_eset
+       		$result_html
+			$result_html.files_path
+		/${__tool_directory__}/AffyQCnormalization_tpl.html
+		]]>
+		</command>
+	
+		<inputs>
+	
+		<param name="inputs" type="data" format="cel" multiple="true" label=".CEL files" help=".CEL files to be used"/>
+
+		<param name="normalization" type="select" label="Preprocessing/normalization">
+		
+    		<option value="rma">rma (backgroung correction + quantile normalization + log2)</option>
+            <option value="quantile">quantile normalization + log2</option>
+            <option value="background">background correction + log2</option>
+            <option value="log2">log2 only</option>
+           
+		
+		</param>
+		
+	</inputs>
+	<outputs>
+		<data format="rdata" name="result_export_eset" label="export normalized expressionSet"/>		
+		<data format="html" name="result_html" label="QC result"/>
+	</outputs>
+
+	<help>
+<![CDATA[
+		**What it does** 
+		    	
+The QCnormalization tool offers to ensure the quality of the data and to normalize them. Several normalization methods are available :
+
+* rma normalization 
+* quantile normalization + log2
+* background correction + log2
+* log2 only
+
+**Results**
+
+- Several quality figures : microarray images, boxplots and MA plots
+- Rdata object containing the normalized data for further analysis
+  		
+]]>
+</help>
+
+</tool>