root/galaxy-central/tools/regVariation/t_test_two_samples.xml

リビジョン 2, 4.7 KB (コミッタ: hatakeyama, 14 年 前)

import galaxy-central

行番号 
1<tool id="t_test_two_samples" name="T Test for Two Samples" version="1.0.0">
2  <description></description>
3 
4  <command interpreter="perl">
5        t_test_two_samples.pl $inputFile1 $inputFile2 $inputTestSidedness3 $inputStandardDeviationEquality4 $outputFile1
6  </command>
7
8  <inputs>
9        <param format="tabular" name="inputFile1" type="data" label="Select the first sample tabular file"/>
10        <param format="tabular" name="inputFile2" type="data" label="Select the second sample tabular file"/>
11       
12    <param name="inputTestSidedness3" type="select" label="Choose the test sidedness:">
13        <option value="two-sided">Two-sided</option>
14        <option value="one-sided:_m1_less_than_m2">One-sided: m1 less than m2</option>
15        <option value="one-sided:_m1_greater_than_m2">One-sided: m1 greater than m2</option>
16    </param>
17   
18    <param name="inputStandardDeviationEquality4" type="select" label="Choose the standard deviation equality status of the two populations:">
19        <option value="equal">Equal</option>
20        <option value="unequal">Unequal</option>
21    </param>
22  </inputs>
23 
24  <outputs>
25    <data format="text" name="outputFile1"/>
26  </outputs>
27 
28  <tests>
29        <test>
30                <param name="inputFile1" value="sample1.tabular" ftype="tabular" />
31                <param name="inputFile2" value="sample2.tabular" ftype="tabular" />
32        <param name="inputTestSidedness3" value="Two-sided" />
33        <param name="inputStandardDeviationEquality4" value="Equal" />
34        <output name="outputFile1" file="t_test_result1.text" />
35        </test>
36       
37        <test>
38                <param name="inputFile1" value="sample1.tabular" ftype="tabular" />
39                <param name="inputFile2" value="sample2.tabular" ftype="tabular" />
40        <param name="inputTestSidedness3" value="Two-sided" />
41        <param name="inputStandardDeviationEquality4" value="Unequal" />
42        <output name="outputFile1" file="t_test_result2.text" />
43        </test>
44       
45        <test>
46                <param name="inputFile1" value="sample1.tabular" ftype="tabular" />
47                <param name="inputFile2" value="sample2.tabular" ftype="tabular" />
48        <param name="inputTestSidedness3" value="One-sided: m1 less than m2" />
49        <param name="inputStandardDeviationEquality4" value="Equal" />
50        <output name="outputFile1" file="t_test_result3.text" />
51        </test>
52       
53        <test>
54                <param name="inputFile1" value="sample1.tabular" ftype="tabular" />
55                <param name="inputFile2" value="sample2.tabular" ftype="tabular" />
56        <param name="inputTestSidedness3" value="One-sided: m1 less than m2" />
57        <param name="inputStandardDeviationEquality4" value="Unequal" />
58        <output name="outputFile1" file="t_test_result4.text" />
59        </test>
60       
61        <test>
62                <param name="inputFile1" value="sample1.tabular" ftype="tabular" />
63                <param name="inputFile2" value="sample2.tabular" ftype="tabular"/>
64        <param name="inputTestSidedness3" value="One-sided: m1 greater than m2" />
65        <param name="inputStandardDeviationEquality4" value="Equal" />
66        <output name="outputFile1" file="t_test_result5.text" />
67        </test>
68       
69        <test>
70                <param name="inputFile1" value="sample1.tabular" ftype="tabular" />
71                <param name="inputFile2" value="sample2.tabular" ftype="tabular" />
72        <param name="inputTestSidedness3" value="One-sided: m1 greater than m2" />
73        <param name="inputStandardDeviationEquality4" value="Unequal" />
74        <output name="outputFile1" file="t_test_result6.text" />
75        </test>
76  </tests>
77
78
79  <help>
80
81.. class:: infomark
82
83**What it does**
84
85This program implements the non-pooled t-test for two samples where the alternative hypothesis is two-sided or one-sided. The program takes four inputs:
86
87- The first input file is a TABULAR format file representing the first sample and consisting of one column only.
88- The second input file is a TABULAR format file representing the first sample and consisting of one column only.
89- The third input is the sidedness of the t-test: either two-sided or, one-sided with m1 less than m2 or, one-sided with m1 greater than m2.
90- The fourth input is the equality status of the standard deviations of both populations.
91- The output file is a TXT file representing the result of the two-sample t-test.
92
93
94**Example**
95
96Let us have the first input file representing the first sample as follows::
97
98        5
99        4
100        8
101        6
102        7
103        2
104        1
105        1
106        0
107        6
108        4
109        5
110        7
111        5
112        3
113        2
114        5
115        8
116        7
117        6
118        4
119
120And the second input file representing the second sample as follows::
121
122        2
123        3
124        5
125        1
126        2
127        7
128        5
129        4
130        3
131        2
132        7
133        6
134        0
135        8
136        4
137        6
138        9
139        2
140        4
141        5
142        6
143
144Runnig the program and choosing "Two-sided" and "Equal" as parameters will give the following output::
145
146        Two Sample t-test
147
148        data:  sample1 and sample2
149        t = -0.3247, df = 40, p-value = 0.7471
150        alternative hypothesis: true difference in means is not equal to 0
151        95 percent confidence interval:
152        -1.720030  1.243839
153        sample estimates:
154        mean of x mean of y
155        4.333333  4.571429
156
157
158  </help> 
159 
160</tool>
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