|
0
|
1 <tool id="normalize_matrix" name="Normalize Matrix" force_history_refresh="True">
|
|
|
2 <command interpreter="python">normalize.matrix.py
|
|
|
3 -d $dataset
|
|
|
4 -r ${center_rows}
|
|
|
5 -c ${center_cols}
|
|
|
6 -R ${var_adj_rows}
|
|
|
7 -C ${var_adj_cols}
|
|
|
8 -o ${output}
|
|
|
9
|
|
|
10 </command>
|
|
|
11 <inputs>
|
|
|
12 <param name="dataset" type="data" format='tabular' label="Data Set" help="Matrix to be normalized (tab-delimited format)"/>
|
|
|
13 <param name="center_rows" type="select" label="Center Rows" help="Centering Method for Rows">
|
|
|
14 <option value="none">No Centering</option>
|
|
|
15 <option value="mean">Mean</option>
|
|
|
16 <option value="median" selected="true">Median</option>
|
|
|
17 </param>
|
|
|
18
|
|
|
19 <param name="center_cols" type="select" label="Center Columns" help="Centering Method for Columns" >
|
|
|
20 <option value="none" selected="true">No Centering</option>
|
|
|
21 <option value="mean">Mean</option>
|
|
|
22 <option value="median">Median</option>
|
|
|
23 </param>
|
|
|
24
|
|
|
25 <param name="var_adj_rows" type="select" label="Variance Adjustment for Rows" help="Variance Adjustment Method for Rows" >
|
|
|
26 <option value="none" selected="true">No Adjustment</option>
|
|
|
27 <option value="mad">Median Absolute Deviation</option>
|
|
|
28 <option value="sd">Standard Deviation</option>
|
|
|
29 </param>
|
|
|
30 <param name="var_adj_cols" type="select" label="Variance Adjustment for Columns" help="Variance Adjustment Method for Columns" >
|
|
|
31 <option value="none" selected="true">No Adjustment</option>
|
|
|
32 <option value="mad">Median Absolute Deviation</option>
|
|
|
33 <option value="sd">Standard Deviation</option>
|
|
|
34 </param>
|
|
|
35
|
|
|
36 </inputs>
|
|
|
37 <outputs>
|
|
|
38 <data format="tabular" name="output" label="Normalized Matrix"/>
|
|
|
39 </outputs>
|
|
|
40 <help>
|
|
|
41 .. class:: infomark
|
|
|
42
|
|
|
43 **Normalize Matrix - Tool to normalize a matrix**
|
|
|
44
|
|
|
45 ----
|
|
|
46
|
|
|
47 **Parameters**
|
|
|
48
|
|
|
49 - **Center Rows** Centering Method for Rows
|
|
|
50
|
|
|
51 * No Centering
|
|
|
52 * Mean
|
|
|
53 * Median
|
|
|
54
|
|
|
55 - **Center Rows** Centering Method for Columns
|
|
|
56
|
|
|
57 * No Centering
|
|
|
58 * Mean
|
|
|
59 * Median
|
|
|
60
|
|
|
61 - **Variance Adjustment for Rows** Variance Adjustment Method for Rows
|
|
|
62
|
|
|
63 * No Adjustment
|
|
|
64 * Median Absolute Deviation
|
|
|
65 * Standard Deviation
|
|
|
66
|
|
|
67 - **Variance Adjustment for Rows** Variance Adjustment Method for Columns
|
|
|
68
|
|
|
69 * No Adjustment
|
|
|
70 * Median Absolute Deviation
|
|
|
71 * Standard Deviation
|
|
|
72
|
|
|
73 </help>
|
|
|
74 </tool>
|
