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Imported from capsule None
author sblanck
date Wed, 13 Apr 2016 07:40:02 -0400
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<tool id="QCnormalization" name="QCnormalization" version="0.1.0">
	<description>Quality control and normalization of affymetric expression data</description>
	<requirements>
	  <container type="docker">sblanck/testtool:latest</container>
	</requirements>
	<command>

		/galaxy-tools/stderr_wrapper.py Rscript 
		/galaxy-tools/transcriptomics/AffyQCnormalization/AffyQCnormalization.R
		   	#for $input in $inputs
                "${input}"
			    "${input.name}"
     		#end for
			"${normalization}"
			$result_export_eset
       		$result_html
			$result_html.files_path
		/galaxy-tools/transcriptomics/AffyQCnormalization/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 expressionSet"/>		
		<data format="html" name="result_html" label="QC result"/>
	</outputs>

	<help>
	</help>

</tool>