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<tool id="Get_Normalized_Expressions" name="Get Normalized Expressions" version="1.0.1">
  <description>Calculate normalization factors and get the normalized expression matrix</description>

    <macros>
        <import>macros.xml</import>
    </macros>

    <expand macro="requirements"/>
    <expand macro="stdio"/>

	<command>R --quiet --slave --file=$__tool_directory__/GetNormalizedExpression.R --args $Gene_Expression $First_Row_Sample_Names $output $Boxplots $Sizes </command>
  <inputs>
		<param name="Gene_Expression" type="data" format="tabular" label="Gene Expression (tab delimited)"/>
		<param name="First_Row_Sample_Names" type="select" format="text">
			<label>The First Row is Sample Names?</label>
			<option value="y">Yes</option>
			<option value="n">No</option>
			</param>
  </inputs>
  <outputs>
		<data format="tabular" name="output" label="Normalized expression"/>
		<data format="pdf" name="Boxplots" label="Boxplots"/>
		<data format="tabular" name="Sizes" label="Normalization factors"/>
  </outputs>

  <help>
The function would provide the normalized expression values (normalized by the library size factors) and estimated library size factors.
A boxplot for checking will also be generated.

</help>


    <expand macro="citation" />

</tool>