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