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1 <tool id="normalize_matrix" name="Normalize Matrix" force_history_refresh="True">
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2 <command interpreter="python">normalize.matrix.py
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3 -d $dataset
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4 -r ${center_rows}
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5 -c ${center_cols}
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6 -R ${var_adj_rows}
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7 -C ${var_adj_cols}
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8 -o ${output}
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9
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10 </command>
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11 <inputs>
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12 <param name="dataset" type="data" format='tabular' label="Data Set" help="Matrix to be normalized (tab-delimited format)"/>
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13 <param name="center_rows" type="select" label="Center Rows" help="Centering Method for Rows">
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14 <option value="none">No Centering</option>
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15 <option value="mean">Mean</option>
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16 <option value="median" selected="true">Median</option>
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17 </param>
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18
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19 <param name="center_cols" type="select" label="Center Columns" help="Centering Method for Columns" >
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20 <option value="none" selected="true">No Centering</option>
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21 <option value="mean">Mean</option>
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22 <option value="median">Median</option>
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23 </param>
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24
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25 <param name="var_adj_rows" type="select" label="Variance Adjustment for Rows" help="Variance Adjustment Method for Rows" >
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26 <option value="none" selected="true">No Adjustment</option>
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27 <option value="mad">Median Absolute Deviation</option>
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28 <option value="sd">Standard Deviation</option>
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29 </param>
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30 <param name="var_adj_cols" type="select" label="Variance Adjustment for Columns" help="Variance Adjustment Method for Columns" >
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31 <option value="none" selected="true">No Adjustment</option>
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32 <option value="mad">Median Absolute Deviation</option>
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33 <option value="sd">Standard Deviation</option>
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34 </param>
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35
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36 </inputs>
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37 <outputs>
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38 <data format="tabular" name="output" label="Normalized Matrix"/>
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39 </outputs>
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40 <help>
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41 .. class:: infomark
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42
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43 **Normalize Matrix - Tool to normalize a matrix**
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44
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45 ----
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46
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47 **Parameters**
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48
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49 - **Center Rows** Centering Method for Rows
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50
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51 * No Centering
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52 * Mean
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53 * Median
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54
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55 - **Center Rows** Centering Method for Columns
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56
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57 * No Centering
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58 * Mean
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59 * Median
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60
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61 - **Variance Adjustment for Rows** Variance Adjustment Method for Rows
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62
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63 * No Adjustment
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64 * Median Absolute Deviation
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65 * Standard Deviation
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66
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67 - **Variance Adjustment for Rows** Variance Adjustment Method for Columns
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68
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69 * No Adjustment
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70 * Median Absolute Deviation
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71 * Standard Deviation
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72
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73 </help>
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74 </tool>
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