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1 <?xml version='1.1' encoding='utf-8'?>
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2 <tool id="Matrix_Transformations" name="Matrix Transformations" version="2.2">
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3 <description> by Rows, Columns, All by method</description>
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4 <command interpreter="python">Matrix_Transformations.py '$p_input' '$extra.choice' '$extra.axes' '$extra.scalevalue' '$extra.offsetvalue' '$output_file'</command>
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5
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6 <inputs>
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7 <conditional name="extra">
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8 <param name="choice" type="select" label="Choose Normalization Method">
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9 <option value="mean_center_normalization">Mean Centered Normalization</option>
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10 <option value="median_center_normalization">Median Centered Normalization</option>
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11 <option value="ln_normalization">Log2 Normalization w offset</option>
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12 <option value="log_normalization">Log10 Normalization w offset</option>
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13 <option value="z_score_normalization">Z-Score Normalization</option>
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14 <option value="transpose">Matrix Transpose</option>
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15 <option value="add_offset">Add Offset Value</option>
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16 <option value="scale">Scale by Multiple</option>
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17 <option value="divide_by_sum">Divide by Sum</option>
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18 </param>
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19 <when value="add_offset">
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20 <param name="offsetvalue" type="text" size="10" value="0.0" label="Matrix Values offset" help="Add value to each Matrix element."/>
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21 <param name="scalevalue" type="text" size="10" hidden="true" value="1.0"/>
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22 <param name="axes" type="text" size="10" hidden="true" value="neither"/>
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23 </when>
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24 <when value="scale">
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25 <param name="scalevalue" type="text" size="10" value="1.0" label="Matrix Value scaling" help="multiply value with each Matrix element."/>
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26 <param name="offsetvalue" type="text" size="10" hidden="true" value="0"/>
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27 <param name="axes" type="text" size="10" hidden="true" value="neither"/>
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28 </when>
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29 <when value="ln_normalization">
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30 <param name="offsetvalue" type="text" size="10" value="0.0" label="Matrix Values offset" help="Calculate log2 for each Matrix element then add offset."/>
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31 <param name="scalevalue" type="text" size="10" hidden="true" value="1.0"/>
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32 <param name="axes" type="select" label="Choose Axis">
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33 <option value="Row">Row</option>
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34 <option value="Column">Column</option>
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35 </param>
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36 </when>
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37 <when value="log_normalization">
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38 <param name="offsetvalue" type="text" size="10" value="0.0" label="Matrix Values offset" help="Calculate log10 for each Matrix element then add offset."/>
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39 <param name="scalevalue" type="text" size="10" hidden="true" value="1.0"/>
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40 <param name="axes" type="select" label="Choose Axis">
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41 <option value="Row">Row</option>
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42 <option value="Column">Column</option>
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43 </param>
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44 </when>
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45 <when value="z_score_normalization">
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46 <param name="offsetvalue" type="text" size="10" hidden="true" value="0"/>
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47 <param name="scalevalue" type="text" size="10" hidden="true" value="1.0"/>
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48 <param name="axes" type="select" label="Choose Axis">
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49 <option value="Row">Row</option>
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50 <option value="Column">Column</option>
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51 </param>
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52 </when>
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53 <when value="mean_center_normalization">
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54 <param name="offsetvalue" type="text" size="10" hidden="true" value="0"/>
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55 <param name="scalevalue" type="text" size="10" hidden="true" value="1.0"/>
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56 <param name="axes" type="select" label="Choose Axis">
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57 <option value="Row">Row</option>
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58 <option value="Column">Column</option>
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59 </param>
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60 </when>
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61 <when value="median_center_normalization">
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62 <param name="offsetvalue" type="text" size="10" hidden="true" value="0"/>
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63 <param name="scalevalue" type="text" size="10" hidden="true" value="1.0"/>
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64 <param name="axes" type="select" label="Choose Axis">
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65 <option value="Row">Row</option>
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66 <option value="Column">Column</option>
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67 </param>
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68 </when>
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69 <when value="transpose">
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70 <param name="offsetvalue" type="text" size="10" hidden="true" value="0"/>
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71 <param name="scalevalue" type="text" size="10" hidden="true" value="1.0"/>
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72 <param name="axes" type="text" size="10" hidden="true" value="neither"/>
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73 </when>
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74 <when value="divide_by_sum">
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75 <param name="offsetvalue" type="text" size="10" hidden="true" value="0"/>
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76 <param name="scalevalue" type="text" size="10" hidden="true" value="1.0"/>
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77 <param name="axes" type="select" label="Choose Axis">
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78 <option value="Row">Row</option>
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79 <option value="Column">Column</option>
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80 </param>
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81 </when>
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82 </conditional>
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83
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84 <param name="p_input" type="data" format="tabular" label="Input Matrix"> </param>
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85
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86 <!-- need scipy!!!!
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87 <option value="rank">Rank Normalization</option>
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88 <when value="rank">
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89 <param name="offsetvalue" type="text" size="10" hidden="true" value="0"/>
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90 <param name="scalevalue" type="text" size="10" hidden="true" value="1.0"/>
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91 </when>
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92
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93 <param name="axes" type="select" label="Choose Axis">
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94 <option value="Row">Row</option>
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95 <option value="Column">Column</option>
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96 </param>
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97 -->
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98 </inputs>
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99
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100
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101
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102 <outputs>
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103 <data name="output_file" format="tabular" />
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104 </outputs>
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105
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106 </tool> |
