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1 <tool id="Get_Normalized_Expressions" name="Get Normalized Expressions" version="1.0.1">
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2 <description>Calculate normalization factors and get the normalized expression matrix</description>
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3
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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7
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8 <expand macro="requirements"/>
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9 <expand macro="stdio"/>
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10
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11 <command>R --quiet --slave --file=$__tool_directory__/GetNormalizedExpression.R --args $Gene_Expression $First_Row_Sample_Names $output $Boxplots $Sizes </command>
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12 <inputs>
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13 <param name="Gene_Expression" type="data" format="tabular" label="Gene Expression (tab delimited)"/>
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14 <param name="First_Row_Sample_Names" type="select" format="text">
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15 <label>The First Row is Sample Names?</label>
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16 <option value="y">Yes</option>
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17 <option value="n">No</option>
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18 </param>
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19 </inputs>
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20 <outputs>
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21 <data format="tabular" name="output" label="Normalized expression"/>
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22 <data format="pdf" name="Boxplots" label="Boxplots"/>
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23 <data format="tabular" name="Sizes" label="Normalization factors"/>
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24 </outputs>
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25
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26 <help>
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27 The function would provide the normalized expression values (normalized by the library size factors) and estimated library size factors.
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28 A boxplot for checking will also be generated.
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29
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30 </help>
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31
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32
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33 <expand macro="citation" />
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34
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35 </tool>
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