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/tools/regVariation/t_test_two_samples.xml

https://bitbucket.org/cistrome/cistrome-harvard/
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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
 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>