Mercurial > repos > pmac > normalizemediannegcntrl

comparison normalizeMedianNegCntrl.xml @ 0:087ab474dfa4 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author pmac
date Wed, 01 Jun 2016 03:52:52 -0400
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:087ab474dfa4
1 <tool id="normalizeMedianNegCntrl" name="Normalize Using Median Negative Controls" version="1.0.0">
2
3 <command interpreter="perl">
4 normalizeMedianNegCntrl.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="normalized_using_median.tabular"/>
21 </test>
22 </tests>
23
24 <help>
25
26 .. class:: infomark
27
28 **What it does**
29
30 This program takes a linear plate table and a plate config file as input and then normalizes each plate in the table to the negative controls in the config.
31 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**.
32
33 **Example**
34
35 If the plates table consisted of::
36
37 #Well Table_1 Table_2
38 A01 1654 6
39 A02 1719 8
40 A03 1624 19
41 A04 1518 6
42 A05 1587 12
43 A06 1517 8
44 A07 1638 9
45 A08 1733 7
46 A09 1617 6
47 A10 1722 8
48 ...
49 P14 1630 6
50 P15 1576 6
51 P16 1740 7
52 P17 1578 6
53 P18 1544 6
54 P19 1692 6
55 P20 1560 6
56 P21 1552 6
57 P22 1790 7
58 P23 1537 6
59 P24 NA NA
60
61 and the plates config was::
62
63 #Well Type Name
64 A02 negcontr NT2
65 B02 negcontr NT2
66 C02 poscontr ASCIZ
67 D02 poscontr PARP
68 E02 negcontr NT2
69 F02 poscontr ASCIZ
70 G02 poscontr PARP
71 H02 negcontr NT2
72 I02 poscontr ASCIZ
73 J02 poscontr PARP
74 K02 negcontr NT2
75 L02 poscontr ASCIZ
76 M02 poscontr PARP
77 N02 negcontr NT2
78 O02 poscontr ASCIZ
79 P02 negcontr NT2
80 A23 negcontr NT2
81 B23 negcontr NT2
82 C23 poscontr ASCIZ
83 D23 poscontr PARP
84 E23 negcontr NT2
85 F23 poscontr ASCIZ
86 G23 poscontr PARP
87 H23 negcontr NT2
88 I23 poscontr ASCIZ
89 J23 poscontr PARP
90 K23 negcontr NT2
91 L23 poscontr ASCIZ
92 M23 poscontr PARP
93 N23 negcontr NT2
94 O23 poscontr ASCIZ
95 P23 negcontr NT2
96 A01 exclude exclude
97 A24 exclude exclude
98 B01 exclude exclude
99 B24 exclude exclude
100 C01 exclude exclude
101 C24 exclude exclude
102 D01 exclude exclude
103 D24 exclude exclude
104 E01 exclude exclude
105 E24 exclude exclude
106 F01 exclude exclude
107 F24 exclude exclude
108 G01 exclude exclude
109 G24 exclude exclude
110 H01 exclude exclude
111 H24 exclude exclude
112 I01 exclude exclude
113 I24 exclude exclude
114 J01 exclude exclude
115 J24 exclude exclude
116 K01 exclude exclude
117 K24 exclude exclude
118 L01 exclude exclude
119 L24 exclude exclude
120 M01 exclude exclude
121 M24 exclude exclude
122 N01 exclude exclude
123 N24 exclude exclude
124 O01 exclude exclude
125 O24 exclude exclude
126 P01 exclude exclude
127 P24 exclude exclude
128
129 Running the program will give the following output::
130
131 #Well Table_1 Table_2
132 A01 1.03 0.75
133 A02 1.07 1
134 A03 1.02 2.38
135 A04 0.95 0.75
136 A05 0.99 1.5
137 A06 0.95 1
138 A07 1.02 1.12
139 A08 1.08 0.88
140 A09 1.01 0.75
141 A10 1.08 1
142 ...
143 P14 1.02 0.75
144 P15 0.99 0.75
145 P16 1.09 0.88
146 P17 0.99 0.75
147 P18 0.97 0.75
148 P19 1.06 0.75
149 P20 0.98 0.75
150 P21 0.97 0.75
151 P22 1.12 0.88
152 P23 0.96 0.75
153 P24 NA NA
154
155 </help>
156
157 </tool>