annotate transformation_config.xml @ 0:eacea1349a7c draft

planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit 83f2d1045c0bf086bbe2de5204cd5c1d8354116f

<tool id="Transformation" name="Transformation" version="2.0.2; 2016-07-27">
	<description>Transforms the dataMatrix intensity values</description>

	<requirements>
	  <requirement type="package" version="3.2.2">R</requirement>
	  <requirement type="package">r-batch</requirement>
	</requirements>
	
	<command><![CDATA[
	Rscript $__tool_directory__/transformation_wrapper.R
			dataMatrix_in "$dataMatrix_in"
			method "$method"
			
			dataMatrix_out "$dataMatrix_out"
			information "$information"
	]]></command>
  
	<inputs>
		<param name="dataMatrix_in" type="data" label="Data matrix file" help="" format="tabular" />
		<param name="method" label="Method" type="select" help="">
			<option value="log2">log2</option>
			<option value="log10">log10</option>
		</param>
	</inputs>

	<outputs>
		<data name="dataMatrix_out" label="${tool.name}_${dataMatrix_in.name}" format="tabular" ></data>
		<data name="information" label="${tool.name}_information.txt" format="txt"/>
	</outputs>
	
	<tests>
	  <test>
            <param name="dataMatrix_in" value="input-dataMatrix.tsv"/>
            <param name="method" value="log10"/>
            <output name="dataMatrix_out" file="output-dataMatrix.tsv"/>
	  </test>
	</tests>
	
	<help>

.. class:: infomark

**Author** Etienne Thevenot (W4M Core Development Team, MetaboHUB Paris, CEA)

---------------------------------------------------

.. class:: infomark

**Tool updates**

See the **NEWS** section at the bottom of this page
  
---------------------------------------------------

========================
Transformation
========================

-----------
Description
-----------

 | Performs transformation of the dataMatrix intensity values aimed at stabilizing variance.
 | For mass spectrometry data, where multiplicative noise has been reported, logarithm transformation can be useful to make the peak intensity variance independent of the intensity mean (see for example Veselkov et al, 2011).
 | For the logarithm transformations, log(1+X) is used (to avoid returning -Inf for 0 values); NA values remain unchanged
 
| `Veselkov et al (2011). Optimized Preprocessing of Ultra-Performance Liquid Chromatography/Mass Spectrometry Urinary Metabolic Profiles for Improved Information Recovery. Analytical Chemistry, 83:5864-5872. &lt;http://dx.doi.org/10.1021/ac201065j&gt;`_

-----------------
Workflow position
-----------------

| In the workflow example below, the intensities are first transformed, before the signal drift and batch-effects are corrected; finally, the data quality is evaluated numerically and visually.
|

.. image:: transformation_workflowPositionImage.png
        :width: 600



-----------
Input files
-----------

+----------------------------+---------+
| Parameter : num + label    |  Format |
+============================+=========+
| 1 : Data matrix file       | tabular |
+----------------------------+---------+

|
| **Required format for the dataMatrix is described in the HowTo entitled 'Format Data For Postprocessing' available on the main page of Workflow4Metabolomics.org**
|

----------
Parameters
----------
	  
Method
	| Method to be used for transforming the intensity values of the dataMatrix:
	| **log2** (resp. **log10**): intensities values are log2 (resp. log10) transformed: log(1+X) is used to avoid generating -Inf for 0 values
	| in case of negative intensities in the initial dataMatrix, an error is returned
	| in case of missing (NA) intensities in the initial dataMatrix, these intensities remain set to NA after transformation

------------
Output files
------------

dataMatrix_out.tabular
	| dataMatrix data file with the transformed intensity values
	| 

information.txt
	| Text file giving some informations about the computation (eg, number of NA and 0 values in the initial dataMatrix)
	|

---------------------------------------------------

---------------
Working example
---------------

.. class:: infomark

See the **W4M00001b_sacurine-complete** shared history in the **Shared Data/Published Histories** menu

---------------------------------------------------

----
NEWS
----

CHANGES IN VERSION 2.0.2
========================

INTERNAL MODIFICATIONS

Creating tests for R code

  </help>

  <citations>
    <citation type="bibtex">@Article{Thevenot2015,
  Title                    = {Analysis of the human adult urinary metabolome variations with age, body mass index and gender by implementing a comprehensive workflow for univariate and OPLS statistical analyses},
  Author                   = {Thévenot, Etienne A. and Roux, Aurélie and Xu, Ying and Ezan, Eric and Junot, Christophe},
  Journal                  = {Journal of Proteome Research},
  Year                     = {2015},
  Note                     = {PMID: 26088811},
  Number                   = {8},
  Pages                    = {3322-3335},
  Volume                   = {14},

  Doi                      = {10.1021/acs.jproteome.5b00354},
  Url                      = {http://pubs.acs.org/doi/full/10.1021/acs.jproteome.5b00354}
}</citation>

</citations>
  
Input files
===========

| **To generate the "dataMatrix":**
|   **1) copy/paste the values below in a .txt files**
|   **2) use the "Get Data" / "Upload File" in the "Tools" (left) panel from the Galaxy / ABiMS page by choosing:**
|     **Set the option 'Convert spaces to tabs' to 'Yes'**
| 

**dataMatrix file**::

	dataMatrix HU_017 HU_021 HU_027 HU_032 HU_041 HU_048 HU_049 HU_050 HU_052 HU_059 HU_060 HU_066 HU_072 HU_077 HU_090 HU_109 HU_110 HU_125 HU_126 HU_131 HU_134 HU_149 HU_150 HU_173 HU_179 HU_180 HU_182 HU_202 HU_204 HU_209
	HMDB01032 2569204.92420381 0 NA 1258838.24348419 13039543.0754619 1909391.77026598 3495.09386434063 2293521.90928998 128503.275117713 81872.5276382213 8103557.56578035 149574887.036181 1544036.41049333 7103429.53933206 14138796.50382 NA 263054.73056162 1671332.30008058 88433.1944958815 23602331.2894815 18648126.5206986 1554657.98756878 34152.3646391152 209372.71275317 33187733.370626 202438.591636003 13581070.0886437 354170.810678102 9120781.48986975 43419175.4051586
	HMDB03072 3628416.30251025 65626.9834353751 112170.118946651 3261804.34422417 42228.2787747563 343254.201250707 1958217.69317664 11983270.0435677 5932111.41638028 5511385.83359531 9154521.47755199 2632133.21209418 9500411.14556502 6551644.51726592 7204319.80891836 1273412.04795188 0 8932005.5351622 8340827.52597275 NA 11217839.169041 5919262.81433556 11790077.0657915 9567977.80797097 73717.5811684739 9991787.29074293 4208098.14739633 623970.649925847 10904221.2642849 2171793.93621067
	HMDB00792 429568.609438384 3887629.50527037 1330692.11658995 1367446.73023821 844197.447472453 2948090.71886592 1614157.90566884 3740009.19379795 3292251.66531919 2310688.79492013 4404239.59008605 3043289.12780863 825736.467181043 2523241.91730649 NA 474901.604069803 0 2955990.64049134 1917716.3427982 1767962.67737699 5926203.40397675 1639065.69474684 346810.763557826 1054776.22313737 2390258.27543894 1831346.37315857 1026696.36904362 7079792.50047866 4368341.01359769 3495986.87280275

  
</tool>