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

<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>