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1 <tool id="normalize_matrix_by_other" name="Normalize Matrix By Other Matrix" force_history_refresh="True">
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2 <command interpreter="python">normalize.matrix.by.other.py
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3 -d ${dataset}
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4 -D ${dataset2}
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5 -c ${ctr_method}
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6
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7 #if str($ctr_method) == "median":
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8 -o ${output_median}
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9 #end if
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10
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11 #if str($ctr_method) == "mean":
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12 -o ${output_mean}
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13 #end if
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14
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15 -r ${return_normalizer_matrix}
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16
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17 #if str($return_normalizer_matrix) == 'yes':
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18 -O ${output_normal}
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19 #end if
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20 </command>
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21 <inputs>
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22 <param name="dataset" type="data" format='tabular' label="Target Data (Matrix to be normalized)" help="Matrix to be normalized (e.g. disease)"/>
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23 <param name="dataset2" type="data" format='tabular' label="Reference Data (Matrix that will be used to normalize other)" help="Matrix to be normalizer (e.g. normals)"/>
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24 <param name="ctr_method" type="select" label="Centering Metric for Genes" help="Specify Metric to Use for Center Rows (Genes)" >
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25 <option value="median" selected="true">Median</option>
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26 <option value="mean">Mean</option>
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27 </param>
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28 <param name="return_normalizer_matrix" type='select' display="radio" label="?" help="Specify whether or not to return a a normalized version of the Reference matrix">
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29 <option value="yes" selected='true' >Yes</option>
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30 <option value="no">No</option>
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31 </param>
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32 </inputs>
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33 <outputs>
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34 <data format="tabular" name="output_median" label="Median Normalized Matrix (by Reference Set)">
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35 <filter>(ctr_method)=="median"</filter>
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36 </data>
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37 <data format="tabular" name="output_mean" label="Mean Normalized Matrix (by Reference Set)">
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38 <filter>(ctr_method)=="mean"</filter>
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39 </data>
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40 <data format="tabular" name="output_normal" label="Normalized Reference Matrix">
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41 <filter>(return_normal_matrix)=="yes"</filter>
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42 </data>
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43 </outputs>
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44 <help>
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45 .. class:: infomark
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46
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47 **Normalize Matrix - Tool to normalize a matrix**
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48
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49 ----
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50
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51 **Parameters**
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52
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53 - **Center Rows** Centering Method for Rows
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54
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55 * No Centering
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56 * Mean
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57 * Median
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58
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59 - **Center Rows** Centering Method for Columns
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60
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61 * No Centering
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62 * Mean
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63 * Median
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64
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65 - **Variance Adjustment for Rows** Variance Adjustment Method for Rows
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66
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67 * No Adjustment
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68 * Median Absolute Deviation
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69 * Standard Deviation
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70
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71 - **Variance Adjustment for Rows** Variance Adjustment Method for Columns
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72
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73 * No Adjustment
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74 * Median Absolute Deviation
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75 * Standard Deviation
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76
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77 </help>
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78 </tool>
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