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> |