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author pmac
date Wed, 01 Jun 2016 03:59:51 -0400
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1 <tool id="robustZScoreNormalization" name="Calculate Robust Z Score Normalization" version="1.0.0">
2 <description>Per Plate</description>
3
4 <command interpreter="perl">
5 robustZScoreNormalization.pl $inputFile1 $inputFile2 $outputFile1
6 </command>
7
8 <inputs>
9 <param format="tabular" name="inputFile1" type="data" label="Select the linear plates file"/>
10 <param format="tabular" name="inputFile2" type="data" label="Select the plate configuration file"/>
11 </inputs>
12
13 <outputs>
14 <data format="tabular" name="outputFile1"/>
15 </outputs>
16
17 <tests>
18 <test>
19 <param name="inputFile1" value="150615-HR-12015-01A.linear"/>
20 <param name="inputFile2" value="plate_config.txt"/>
21 <output name="outputFile1" file="calc_robust_z.tabular"/>
22 </test>
23 </tests>
24
25
26 <help>
27
28 .. class:: infomark
29
30 **What it does**
31
32 This program takes a linear plate table and a plate config file as input and then performs Robust Z Score Normalization on the data.
33 The plate config file **must** contain the columns Well, Type and Name in that order. Further the data in column Type must be **exclude**, **negcontr** or **poscontr**.
34
35 **Example**
36
37 If the plates table consisted of::
38
39 #Well Table_1 Table_2
40 A01 1654 6
41 A02 1719 8
42 A03 1624 19
43 A04 1518 6
44 A05 1587 12
45 A06 1517 8
46 A07 1638 9
47 A08 1733 7
48 A09 1617 6
49 A10 1722 8
50 ...
51 P14 1630 6
52 P15 1576 6
53 P16 1740 7
54 P17 1578 6
55 P18 1544 6
56 P19 1692 6
57 P20 1560 6
58 P21 1552 6
59 P22 1790 7
60 P23 1537 6
61 P24 NA NA
62
63 and the plates config was::
64
65 #Well Type Name
66 A02 negcontr NT2
67 B02 negcontr NT2
68 C02 poscontr ASCIZ
69 D02 poscontr PARP
70 E02 negcontr NT2
71 F02 poscontr ASCIZ
72 G02 poscontr PARP
73 H02 negcontr NT2
74 I02 poscontr ASCIZ
75 J02 poscontr PARP
76 K02 negcontr NT2
77 L02 poscontr ASCIZ
78 M02 poscontr PARP
79 N02 negcontr NT2
80 O02 poscontr ASCIZ
81 P02 negcontr NT2
82 A23 negcontr NT2
83 B23 negcontr NT2
84 C23 poscontr ASCIZ
85 D23 poscontr PARP
86 E23 negcontr NT2
87 F23 poscontr ASCIZ
88 G23 poscontr PARP
89 H23 negcontr NT2
90 I23 poscontr ASCIZ
91 J23 poscontr PARP
92 K23 negcontr NT2
93 L23 poscontr ASCIZ
94 M23 poscontr PARP
95 N23 negcontr NT2
96 O23 poscontr ASCIZ
97 P23 negcontr NT2
98 A01 exclude exclude
99 A24 exclude exclude
100 B01 exclude exclude
101 B24 exclude exclude
102 C01 exclude exclude
103 C24 exclude exclude
104 D01 exclude exclude
105 D24 exclude exclude
106 E01 exclude exclude
107 E24 exclude exclude
108 F01 exclude exclude
109 F24 exclude exclude
110 G01 exclude exclude
111 G24 exclude exclude
112 H01 exclude exclude
113 H24 exclude exclude
114 I01 exclude exclude
115 I24 exclude exclude
116 J01 exclude exclude
117 J24 exclude exclude
118 K01 exclude exclude
119 K24 exclude exclude
120 L01 exclude exclude
121 L24 exclude exclude
122 M01 exclude exclude
123 M24 exclude exclude
124 N01 exclude exclude
125 N24 exclude exclude
126 O01 exclude exclude
127 O24 exclude exclude
128 P01 exclude exclude
129 P24 exclude exclude
130
131 Running the program will give the following output::
132
133 #Well Table_1 Table_2
134 A01 0.74 -0.67
135 A02 1.55 0.67
136 A03 0.36 8.09
137 A04 -0.96 -0.67
138 A05 -0.1 3.37
139 A06 -0.97 0.67
140 A07 0.54 1.35
141 A08 1.72 0
142 A09 0.27 -0.67
143 A10 1.59 0.67
144 ...
145 P14 0.44 -0.67
146 P15 -0.24 -0.67
147 P16 1.81 0
148 P17 -0.21 -0.67
149 P18 -0.64 -0.67
150 P19 1.21 -0.67
151 P20 -0.44 -0.67
152 P21 -0.54 -0.67
153 P22 2.44 0
154 P23 -0.72 -0.67
155 P24 NA NA
156
157 </help>
158
159 </tool>