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<tool id="QCnormalization" name="QCnormalization" version="0.1.0">

    <description>Quality control and normalization of affymetrix expression data</description>

    <requirements>
        <requirement type="package" version="0.1.0">r-smagexp</requirement>
    </requirements>

    <stdio>
        <exit_code range="1:" />
        <regex match="Warning" source="both" level="warning"/>
    </stdio>

    <command>
        <![CDATA[
        Rscript 
        ${__tool_directory__}/AffyQCnormalization.R
            --input "#for $input in $inputs# $input;$input.name, #end for#"
            --normalization ${normalization}
            --rdataoutput $result_export_eset
            --htmloutput $result_html
            --htmloutputpath $result_html.files_path
            --htmltemplate ${__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>