/tools/regVariation/t_test_two_samples.xml
https://bitbucket.org/cistrome/cistrome-harvard/ · XML · 160 lines · 131 code · 29 blank · 0 comment · 0 complexity · 2b18cac37bf5d18d72a23bc79714a40c MD5 · raw file
- <tool id="t_test_two_samples" name="T Test for Two Samples" version="1.0.0">
- <description></description>
-
- <command interpreter="perl">
- t_test_two_samples.pl $inputFile1 $inputFile2 $inputTestSidedness3 $inputStandardDeviationEquality4 $outputFile1
- </command>
- <inputs>
- <param format="tabular" name="inputFile1" type="data" label="Select the first sample tabular file"/>
- <param format="tabular" name="inputFile2" type="data" label="Select the second sample tabular file"/>
-
- <param name="inputTestSidedness3" type="select" label="Choose the test sidedness:">
- <option value="two-sided">Two-sided</option>
- <option value="one-sided:_m1_less_than_m2">One-sided: m1 less than m2</option>
- <option value="one-sided:_m1_greater_than_m2">One-sided: m1 greater than m2</option>
- </param>
-
- <param name="inputStandardDeviationEquality4" type="select" label="Choose the standard deviation equality status of the two populations:">
- <option value="equal">Equal</option>
- <option value="unequal">Unequal</option>
- </param>
- </inputs>
-
- <outputs>
- <data format="text" name="outputFile1"/>
- </outputs>
-
- <tests>
- <test>
- <param name="inputFile1" value="sample1.tabular" ftype="tabular" />
- <param name="inputFile2" value="sample2.tabular" ftype="tabular" />
- <param name="inputTestSidedness3" value="Two-sided" />
- <param name="inputStandardDeviationEquality4" value="Equal" />
- <output name="outputFile1" file="t_test_result1.text" />
- </test>
-
- <test>
- <param name="inputFile1" value="sample1.tabular" ftype="tabular" />
- <param name="inputFile2" value="sample2.tabular" ftype="tabular" />
- <param name="inputTestSidedness3" value="Two-sided" />
- <param name="inputStandardDeviationEquality4" value="Unequal" />
- <output name="outputFile1" file="t_test_result2.text" />
- </test>
-
- <test>
- <param name="inputFile1" value="sample1.tabular" ftype="tabular" />
- <param name="inputFile2" value="sample2.tabular" ftype="tabular" />
- <param name="inputTestSidedness3" value="One-sided: m1 less than m2" />
- <param name="inputStandardDeviationEquality4" value="Equal" />
- <output name="outputFile1" file="t_test_result3.text" />
- </test>
-
- <test>
- <param name="inputFile1" value="sample1.tabular" ftype="tabular" />
- <param name="inputFile2" value="sample2.tabular" ftype="tabular" />
- <param name="inputTestSidedness3" value="One-sided: m1 less than m2" />
- <param name="inputStandardDeviationEquality4" value="Unequal" />
- <output name="outputFile1" file="t_test_result4.text" />
- </test>
-
- <test>
- <param name="inputFile1" value="sample1.tabular" ftype="tabular" />
- <param name="inputFile2" value="sample2.tabular" ftype="tabular"/>
- <param name="inputTestSidedness3" value="One-sided: m1 greater than m2" />
- <param name="inputStandardDeviationEquality4" value="Equal" />
- <output name="outputFile1" file="t_test_result5.text" />
- </test>
-
- <test>
- <param name="inputFile1" value="sample1.tabular" ftype="tabular" />
- <param name="inputFile2" value="sample2.tabular" ftype="tabular" />
- <param name="inputTestSidedness3" value="One-sided: m1 greater than m2" />
- <param name="inputStandardDeviationEquality4" value="Unequal" />
- <output name="outputFile1" file="t_test_result6.text" />
- </test>
- </tests>
- <help>
- .. class:: infomark
- **What it does**
- 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:
- - The first input file is a TABULAR format file representing the first sample and consisting of one column only.
- - The second input file is a TABULAR format file representing the first sample and consisting of one column only.
- - 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.
- - The fourth input is the equality status of the standard deviations of both populations.
- - The output file is a TXT file representing the result of the two-sample t-test.
- **Example**
- Let us have the first input file representing the first sample as follows::
- 5
- 4
- 8
- 6
- 7
- 2
- 1
- 1
- 0
- 6
- 4
- 5
- 7
- 5
- 3
- 2
- 5
- 8
- 7
- 6
- 4
- And the second input file representing the second sample as follows::
- 2
- 3
- 5
- 1
- 2
- 7
- 5
- 4
- 3
- 2
- 7
- 6
- 0
- 8
- 4
- 6
- 9
- 2
- 4
- 5
- 6
- Runnig the program and choosing "Two-sided" and "Equal" as parameters will give the following output::
- Two Sample t-test
- data: sample1 and sample2
- t = -0.3247, df = 40, p-value = 0.7471
- alternative hypothesis: true difference in means is not equal to 0
- 95 percent confidence interval:
- -1.720030 1.243839
- sample estimates:
- mean of x mean of y
- 4.333333 4.571429
- </help>
-
- </tool>