Mercurial > repos > md-anderson-bioinformatics > matrix_manipulation
comparison Matrix_Transformations.xml @ 1:f1bcd79cd923 draft default tip
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| author | insilico-bob |
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| date | Tue, 27 Nov 2018 14:20:40 -0500 |
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| 0:7f12c81e2083 | 1:f1bcd79cd923 |
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| 1 <?xml version='1.1' encoding='utf-8'?> | |
| 2 <tool id="Matrix_Transformations" name="Matrix Transformations" version="2.2"> | |
| 3 <description> by Rows, Columns, All by method</description> | |
| 4 <command interpreter="python">Matrix_Transformations.py '$p_input' '$extra.choice' '$extra.axes' '$extra.scalevalue' '$extra.offsetvalue' '$output_file'</command> | |
| 5 | |
| 6 <inputs> | |
| 7 <conditional name="extra"> | |
| 8 <param name="choice" type="select" label="Choose Normalization Method"> | |
| 9 <option value="mean_center_normalization">Mean Centered Normalization</option> | |
| 10 <option value="median_center_normalization">Median Centered Normalization</option> | |
| 11 <option value="ln_normalization">Log2 Normalization w offset</option> | |
| 12 <option value="log_normalization">Log10 Normalization w offset</option> | |
| 13 <option value="z_score_normalization">Z-Score Normalization</option> | |
| 14 <option value="transpose">Matrix Transpose</option> | |
| 15 <option value="add_offset">Add Offset Value</option> | |
| 16 <option value="scale">Scale by Multiple</option> | |
| 17 <option value="divide_by_sum">Divide by Sum</option> | |
| 18 </param> | |
| 19 <when value="add_offset"> | |
| 20 <param name="offsetvalue" type="text" size="10" value="0.0" label="Matrix Values offset" help="Add value to each Matrix element."/> | |
| 21 <param name="scalevalue" type="text" size="10" hidden="true" value="1.0"/> | |
| 22 <param name="axes" type="text" size="10" hidden="true" value="neither"/> | |
| 23 </when> | |
| 24 <when value="scale"> | |
| 25 <param name="scalevalue" type="text" size="10" value="1.0" label="Matrix Value scaling" help="multiply value with each Matrix element."/> | |
| 26 <param name="offsetvalue" type="text" size="10" hidden="true" value="0"/> | |
| 27 <param name="axes" type="text" size="10" hidden="true" value="neither"/> | |
| 28 </when> | |
| 29 <when value="ln_normalization"> | |
| 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."/> | |
| 31 <param name="scalevalue" type="text" size="10" hidden="true" value="1.0"/> | |
| 32 <param name="axes" type="select" label="Choose Axis"> | |
| 33 <option value="Row">Row</option> | |
| 34 <option value="Column">Column</option> | |
| 35 </param> | |
| 36 </when> | |
| 37 <when value="log_normalization"> | |
| 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."/> | |
| 39 <param name="scalevalue" type="text" size="10" hidden="true" value="1.0"/> | |
| 40 <param name="axes" type="select" label="Choose Axis"> | |
| 41 <option value="Row">Row</option> | |
| 42 <option value="Column">Column</option> | |
| 43 </param> | |
| 44 </when> | |
| 45 <when value="z_score_normalization"> | |
| 46 <param name="offsetvalue" type="text" size="10" hidden="true" value="0"/> | |
| 47 <param name="scalevalue" type="text" size="10" hidden="true" value="1.0"/> | |
| 48 <param name="axes" type="select" label="Choose Axis"> | |
| 49 <option value="Row">Row</option> | |
| 50 <option value="Column">Column</option> | |
| 51 </param> | |
| 52 </when> | |
| 53 <when value="mean_center_normalization"> | |
| 54 <param name="offsetvalue" type="text" size="10" hidden="true" value="0"/> | |
| 55 <param name="scalevalue" type="text" size="10" hidden="true" value="1.0"/> | |
| 56 <param name="axes" type="select" label="Choose Axis"> | |
| 57 <option value="Row">Row</option> | |
| 58 <option value="Column">Column</option> | |
| 59 </param> | |
| 60 </when> | |
| 61 <when value="median_center_normalization"> | |
| 62 <param name="offsetvalue" type="text" size="10" hidden="true" value="0"/> | |
| 63 <param name="scalevalue" type="text" size="10" hidden="true" value="1.0"/> | |
| 64 <param name="axes" type="select" label="Choose Axis"> | |
| 65 <option value="Row">Row</option> | |
| 66 <option value="Column">Column</option> | |
| 67 </param> | |
| 68 </when> | |
| 69 <when value="transpose"> | |
| 70 <param name="offsetvalue" type="text" size="10" hidden="true" value="0"/> | |
| 71 <param name="scalevalue" type="text" size="10" hidden="true" value="1.0"/> | |
| 72 <param name="axes" type="text" size="10" hidden="true" value="neither"/> | |
| 73 </when> | |
| 74 <when value="divide_by_sum"> | |
| 75 <param name="offsetvalue" type="text" size="10" hidden="true" value="0"/> | |
| 76 <param name="scalevalue" type="text" size="10" hidden="true" value="1.0"/> | |
| 77 <param name="axes" type="select" label="Choose Axis"> | |
| 78 <option value="Row">Row</option> | |
| 79 <option value="Column">Column</option> | |
| 80 </param> | |
| 81 </when> | |
| 82 </conditional> | |
| 83 | |
| 84 <param name="p_input" type="data" format="tabular" label="Input Matrix"> </param> | |
| 85 | |
| 86 <!-- need scipy!!!! | |
| 87 <option value="rank">Rank Normalization</option> | |
| 88 <when value="rank"> | |
| 89 <param name="offsetvalue" type="text" size="10" hidden="true" value="0"/> | |
| 90 <param name="scalevalue" type="text" size="10" hidden="true" value="1.0"/> | |
| 91 </when> | |
| 92 | |
| 93 <param name="axes" type="select" label="Choose Axis"> | |
| 94 <option value="Row">Row</option> | |
| 95 <option value="Column">Column</option> | |
| 96 </param> | |
| 97 --> | |
| 98 </inputs> | |
| 99 | |
| 100 | |
| 101 | |
| 102 <outputs> | |
| 103 <data name="output_file" format="tabular" /> | |
| 104 </outputs> | |
| 105 | |
| 106 </tool> |