annotate compute_q_values.xml @ 2:8b3593b7e5ec draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/compute_q_values commit a1517c9d22029095120643bbe2c8fa53754dd2b7

<tool id="compute_q_values" name="Compute q-values" version="1.0.1">
  <description>based on multiple simultaneous tests p-values</description>
  <requirements>
    <requirement type="package" version="2.11.0">R</requirement>
    <requirement type="package" version="1.34.0">bioc_qvalue</requirement>
  </requirements>
  <command interpreter="perl">
  	compute_q_values.pl $inputFile1 $inputLambda2 $inputPI0_method3 $inputFDR_level4 $inputRobust5 $outputFile1 $outputFile2
  </command>

  <inputs>
  	<param format="tabular" name="inputFile1" type="data" label="Select the p-values file"/>
  	
  	<param type="text" name="inputLambda2" value="sequence_from_0_to_0.95_increment_0.05" label="What is the lambda value?" help="Either choose the default sequence or one deciaml value between 0 and 1"/>
  	
  	<param name="inputPI0_method3" type="select" label="Choose the PI method:">
    	<option value="smoother">smoother</option>
      	<option value="bootstrap">bootstrap</option>
    </param>
    
    <param type="float" name="inputFDR_level4" value="" label="What is the FDR level?" help="The FDR level must be between 0 and 1"/>
    
    <param name="inputRobust5" type="select" label="Do you want to make the estimate more robust:" help="Choose TRUE for small p-values">
  		<option value="FALSE">FALSE</option>
    	<option value="TRUE">TRUE</option>
    </param>
  </inputs>
  
  <outputs>
    <data format="tabular" name="outputFile1"/>
    <data format="pdf" name="outputFile2"/>
  </outputs>

  <tests>
  	<test>
  		<param name="inputFile1" value="p_values.tabular" ftype="tabular" />
    	<param name="inputLambda2" value="sequence_from_0_to_0.95_increment_0.05" />
    	<param name="inputPI0_method3" value="smoother" />
    	<param name="inputFDR_level4" value="0.05" />
    	<param name="inputRobust5" value="FALSE" />
    	<output name="outputFile1" file="q_values.tabular" />
    	<output name="outputFile1" file="p_q_hists_Q_plots.pdf" />
  		</test>
  </tests>
  	
  <help> 

.. class:: infomark

**What it does**

This program computes the q-values based on the p-values of multiple simultaneous tests. The q-values are computed using a specific R package, created by John Storey and Alan Dabney, called "qvalue". The program takes five inputs:
 
- The first input is a TABULAR format file consisting of one column only that represents the p-values of multiple simultaneous tests, one line for every p-value. 
- The second input is the lambda parameter. The user can choose either the default: seq(0, 0.95, 0.05) or a decimal number between 0.0 and 1.0.
- The third input is PI method which is either "smoother" or "bootstrap".
- The fourth input is the FDR (false discovery rate) level which is a decimal number between 0.0 and 1.0.
- The fifth input is either TRUE or FALSE for the estimate robustness. 

The program gives two outputs:

- The first output is a TABULAR format file consisting of three columns: 

 - the left column represents the p-values of multiple simultaneous tests, one line for every p-value
 - the middle column represents the q-values corresponding to the p-values
 - the third column represent the significance values, either 1 for significant or 0 for non-significant 

- The second output is a PDF format file consisting of three pages: 

 - the first page represents the p-values histogram
 - the second page represents the q-values histogram
 - the third page represents the four Q-plots as introduced in the "qvalue" package manual.
  

**Example**

Let us have the first input file of p-values as follows::

	0.140627492
	0.432249886
	0.122120877
	0.142010182
	0.012909858
	0.000142807
	0.039841941
	0.035173303
	0.011340057
	1.01E-05
	0.212738282
	0.091256284
	0.547375415
	0.189589833
	6.18E-12
	0.001235875
	1.10E-05
	9.75E-07
	2.13E-18
	2.54E-16
	1.20E-19
	9.76E-14
	0.359181534
	0.03661672
	0.400459987
	0.387436466
	0.342075061
	0.904129283
	0.031152635

Running the program will give the following output::

	pi0: 0.140311054	

	FDR level: 0.05

	p-value		q-value		significant
	0.1406275	0.02889212	1
	0.4322499	0.06514199	0
	0.1221209	0.02760624	1
	0.1420102	0.02889212	1
	0.01290986	0.00437754	1
	0.000142807	6.46E-05	1
	0.03984194	0.01013235	1
	0.0351733	0.009932946	1
	0.01134006	0.004194811	1
	1.01E-05	5.59E-06	1
	0.2127383	0.03934711	1
	0.09125628	0.02184257	1
	0.5473754	0.07954578	0
	0.1895898	0.03673547	1
	6.18E-12	5.03E-12	1
	0.001235875	0.00050288	1
	1.10E-05	5.59E-06	1
	9.75E-07	6.61E-07	1
	2.13E-18	4.33E-18	1
	2.54E-16	3.45E-16	1
	1.20E-19	4.88E-19	1
	9.76E-14	9.93E-14	1
	0.3591815	0.06089654	0
	0.03661672	0.009932946	1
	0.40046	0.0626723	0
	0.3874365	0.0626723	0
	0.3420751	0.06051785	0
	0.9041293	0.1268593	0
	0.03115264	0.009750824	1
	
	
.. image:: p_hist.png


.. image:: q_hist.png


.. image:: Q_plots.png


  </help>  
  
</tool>