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comparison calculateZPrimeFactor.xml @ 0:8fb3d398725a draft default tip

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author pmac
date Wed, 01 Jun 2016 03:37:27 -0400
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1 <tool id="calculateZPrimeFactor" name="Calculate Z Prime Factor" version="1.0.0">
2
3 <command interpreter="perl">
4 calculateZPrimeFactor.pl $inputFile1 $inputFile2 $outputFile1
5 </command>
6
7 <inputs>
8 <param format="tabular" name="inputFile1" type="data" label="Select the linear plates file"/>
9 <param format="tabular" name="inputFile2" type="data" label="Select the plate configuration file"/>
10 </inputs>
11
12 <outputs>
13 <data format="tabular" name="outputFile1"/>
14 </outputs>
15
16 <tests>
17 <test>
18 <param name="inputFile1" value="150615-HR-12015-01A.linear"/>
19 <param name="inputFile2" value="plate_config.txt"/>
20 <output name="outputFile1" file="calc_z_prime.tabular"/>
21 </test>
22 </tests>
23
24
25 <help>
26
27 .. class:: infomark
28
29 **What it does**
30
31 This program takes a linear plate table and a plate config file and then calculates the Z Prime Factors for your data.
32 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**.
33
34 **Example**
35
36 If the plates table consisted of::
37
38 #Well Table_1 Table_2
39 A01 1654 6
40 A02 1719 8
41 A03 1624 19
42 A04 1518 6
43 A05 1587 12
44 A06 1517 8
45 A07 1638 9
46 A08 1733 7
47 A09 1617 6
48 A10 1722 8
49 ...
50 P14 1630 6
51 P15 1576 6
52 P16 1740 7
53 P17 1578 6
54 P18 1544 6
55 P19 1692 6
56 P20 1560 6
57 P21 1552 6
58 P22 1790 7
59 P23 1537 6
60 P24 NA NA
61
62 and the plates config was::
63
64 #Well Type Name
65 A02 negcontr mock
66 B02 negcontr mock
67 C02 poscontr ASCIZ
68 D02 poscontr PARP
69 E02 negcontr NT2
70 F02 poscontr ASCIZ
71 G02 poscontr PARP
72 H02 negcontr NT2
73 I02 poscontr ASCIZ
74 J02 poscontr PARP
75 K02 negcontr NT2
76 L02 poscontr ASCIZ
77 M02 poscontr PARP
78 N02 negcontr mock
79 O02 poscontr ASCIZ
80 P02 negcontr NT2
81 A23 negcontr mock
82 B23 negcontr mock
83 C23 poscontr ASCIZ
84 D23 poscontr PARP
85 E23 negcontr NT2
86 F23 poscontr ASCIZ
87 G23 poscontr PARP
88 H23 negcontr NT2
89 I23 poscontr ASCIZ
90 J23 poscontr PARP
91 K23 negcontr NT2
92 L23 poscontr ASCIZ
93 M23 poscontr PARP
94 N23 negcontr mock
95 O23 poscontr ASCIZ
96 P23 negcontr NT2
97 A01 exclude exclude
98 A24 exclude exclude
99 B01 exclude exclude
100 B24 exclude exclude
101 C01 exclude exclude
102 C24 exclude exclude
103 D01 exclude exclude
104 D24 exclude exclude
105 E01 exclude exclude
106 E24 exclude exclude
107 F01 exclude exclude
108 F24 exclude exclude
109 G01 exclude exclude
110 G24 exclude exclude
111 H01 exclude exclude
112 H24 exclude exclude
113 I01 exclude exclude
114 I24 exclude exclude
115 J01 exclude exclude
116 J24 exclude exclude
117 K01 exclude exclude
118 K24 exclude exclude
119 L01 exclude exclude
120 L24 exclude exclude
121 M01 exclude exclude
122 M24 exclude exclude
123 N01 exclude exclude
124 N24 exclude exclude
125 O01 exclude exclude
126 O24 exclude exclude
127 P01 exclude exclude
128 P24 exclude exclude
129
130 Running the program will give the following output::
131
132 plate control.duo z.prime.factor
133 Table_1 mock/ASCIZ -64.34
134 Table_2 mock/ASCIZ -Inf
135 Table_1 mock/PARP -10.78
136 Table_2 mock/PARP -0.67
137 Table_1 NT2/ASCIZ -55.97
138 Table_2 NT2/ASCIZ -9.38
139 Table_1 NT2/PARP -16.79
140 Table_2 NT2/PARP -0.32
141
142 </help>
143
144 </tool>