annotate tools/regVariation/t_test_two_samples.xml @ 0:9071e359b9a3

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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 
85 This 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 
96 Let us have the first input file representing the first sample as follows::
97 
98 	5
99 	4
00 	8
01 	6
02 	7
03 	2
04 	1
05 	1
06 	0
07 	6
08 	4
09 	5
10 	7
11 	5
12 	3
13 	2
14 	5
15 	8
16 	7
17 	6
18 	4
19 
20 And the second input file representing the second sample as follows::
21 
22 	2
23 	3
24 	5
25 	1
26 	2
27 	7
28 	5
29 	4
30 	3
31 	2
32 	7
33 	6
34 	0
35 	8
36 	4
37 	6
38 	9
39 	2
40 	4
41 	5
42 	6
43 
44 Runnig the program and choosing "Two-sided" and "Equal" as parameters will give the following output::
45 
46 	Two Sample t-test
47 
48 	data:  sample1 and sample2 
49 	t = -0.3247, df = 40, p-value = 0.7471
50 	alternative hypothesis: true difference in means is not equal to 0 
51 	95 percent confidence interval:
52  	-1.720030  1.243839 
53 	sample estimates:
54 	mean of x mean of y 
55  	4.333333  4.571429 
56 
57 
58   </help>  
59   
60 </tool>