Mercurial > repos > ning > ebseq
comparison GetNormalizedExpression.xml @ 0:e42c12a40df6 draft
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| author | ning |
|---|---|
| date | Fri, 15 Mar 2013 18:18:16 -0400 |
| parents | |
| children | 3eb0e0d10f36 |
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| -1:000000000000 | 0:e42c12a40df6 |
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| 1 <tool id="Get_Normalized_Expressions" name="Get Normalized Expressions"> | |
| 2 <description>Calculate normalization factors and get the normalized expression matrix</description> | |
| 3 <command>R --quiet --slave --file=$GALAXY_ROOT_DIR/tools/EBSeq/GetNormalizedExpression.R --args $Gene_Expression $First_Row_Sample_Names $output $Boxplots $Sizes </command> | |
| 4 <inputs> | |
| 5 <param name="Gene_Expression" type="data" format="tabular" label="Gene Expression (tab eliminated)"/> | |
| 6 <param name="First_Row_Sample_Names" type="select" format="text"> | |
| 7 <label>The First Row is Sample Names?</label> | |
| 8 <option value="y">Yes</option> | |
| 9 <option value="n">No</option> | |
| 10 </param> | |
| 11 </inputs> | |
| 12 <outputs> | |
| 13 <data format="tabular" name="output" /> | |
| 14 <data format="pdf" name="Boxplots" /> | |
| 15 <data format="tabular" name="Sizes" /> | |
| 16 </outputs> | |
| 17 | |
| 18 <help> | |
| 19 The function would provide the normalized expression values (normalized by the library size factors) and estimated library size factors. | |
| 20 A boxplot for checking will also be generated. | |
| 21 | |
| 22 </help> | |
| 23 | |
| 24 | |
| 25 </tool> |