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date Tue, 02 May 2017 09:47:22 -0400
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<tool id="Batch_correction" name="Batch_correction" version="2.1.2">
  <description>Corrects intensities for signal drift and batch-effects</description>

  <requirements>
    <requirement type="package">r-batch</requirement>
    <requirement type="package">r-ade4</requirement>
    <requirement type="package">bioconductor-pcamethods</requirement>
    <requirement type="package">bioconductor-ropls</requirement>
  </requirements>

  <stdio>
    <exit_code range="1:" level="fatal" />
  </stdio>
  
  <command><![CDATA[
    #if str($span_condition.method) == 'all_loess_pool':
        Rscript $__tool_directory__/batch_correction_all_loess_wrapper.R
        dataMatrix "$dataMatrix"
        sampleMetadata "$sampleMetadata"
        variableMetadata "$variableMetadata"
        method "all_loess_pool"
        span "${span_condition.span}"
    
    #elif str($span_condition.method) == 'all_loess_sample':
        Rscript $__tool_directory__/batch_correction_all_loess_wrapper.R
        dataMatrix "$dataMatrix"
        sampleMetadata "$sampleMetadata"
        variableMetadata "$variableMetadata"
        method "all_loess_sample"
        span "${span_condition.span}"
    #else:
        Rscript $__tool_directory__/batch_correction_wrapper.R
        analyse "batch_correction"
        dataMatrix "$dataMatrix"
        sampleMetadata "$sampleMetadata"
        variableMetadata "$variableMetadata"
        method "${span_condition.method}"
        #if str($span_condition.method) == 'linear':
            span "none"
        #else:
            span "${span_condition.span}"
        #end if
	valnull "${span_condition.valnull}"
        ref_factor "${span_condition.ref_factor}"
        detail "${span_condition.detail}"
    #end if
    dataMatrix_out "$dataMatrix_out" variableMetadata_out "$variableMetadata_out"
    graph_output "$graph_output"  rdata_output "$rdata_output"
  ]]></command>

	<inputs>
		<param name="dataMatrix" label="Data Matrix file " format="tabular" type="data" />
		<param name="sampleMetadata" label="Sample metadata file " format="tabular" type="data" help="must contain at least the three following columns: 'batch' + 'injectionOrder' + 'sampleType'"/>
		<param name="variableMetadata" label="Variable metadata file " format="tabular" type="data" />
		
		<conditional name="span_condition">
			<param name="method" label="Type of regression model " type="select" help="To select between linear or non-linear (lowess or loess) methods to be used in Van der Kloet algorithm ; when using loess, you can choose to use pools or samples to model batch effect.">
				<option value="linear">linear</option>
				<option value="lowess">lowess</option>
				<option value="loess">loess</option>
				<option value="all_loess_pool">all loess pool</option>
				<option value="all_loess_sample">all loess sample</option>
			</param>
			<when value="linear">
				<param name="valnull" label="Null values" type="select" display="radio" help="What to do of generated negative or infinite values">
					<option value="0">consider it as a null intensity</option>
					<option value="NA">consider it as a missing value</option>
				</param>
				<param name="ref_factor" label="Factor of interest " type="text"  value="batch" help="column name of factor of interest (often a biological factor); if none, leave 'batch'" />
				<param name="detail" label="Level of details for plots " type="select" help="Amount of plots in the pdf file output. See Help section for more details.">
					<option value="no">basic</option>
					<option value="plot">standard</option>
					<option value="reg">complete</option>
				</param>
			</when>
			<when value="lowess">
				<param name="span" type="float" value="0.85" label="span" help="it is a advanced option. Must be less than or equal to 1"/>
				<param name="valnull" label="Null values" type="select" display="radio" help="What to do of generated negative or infinite values">
					<option value="0">consider it as a null intensity</option>
					<option value="NA">consider it as a missing value</option>
				</param>
				<param name="ref_factor" label="Factor of interest " type="text"  value="batch" help="column name of factor of interest (often a biological factor); if none, leave 'batch'" />
				<param name="detail" label="Level of details for plots " type="select" help="Amount of plots in the pdf file output. See Help section for more details.">
					<option value="no">basic</option>
					<option value="plot">standard</option>
					<option value="reg">complete</option>
				</param>
			</when>
			<when value="loess">
				<param name="span" type="float" value="1" label="span" help="it is a advanced option. Must be strictly greater than 0"/>
				<param name="valnull" label="Null values" type="select" display="radio" help="What to do of generated negative or infinite values">
					<option value="0">consider it as a null intensity</option>
					<option value="NA">consider it as a missing value</option>
				</param>
				<param name="ref_factor" label="Factor of interest " type="text"  value="batch" help="column name of factor of interest (often a biological factor); if none, leave 'batch'" />
				<param name="detail" label="Level of details for plots " type="select" help="Amount of plots in the pdf file output. See Help section for more details.">
					<option value="no">basic</option>
					<option value="plot">standard</option>
					<option value="reg">complete</option>
				</param>
			</when>
			<when value="all_loess_pool">
				<param name="span" type="float" value="1" label="span" help="smoothing parameter; must be > 0"/>
			</when>
			<when value="all_loess_sample">
				<param name="span" type="float" value="1" label="span" help="smoothing parameter; must be > 0"/>
			</when>
		</conditional>
	</inputs>
	
	<outputs>
		<data name="dataMatrix_out" label="${tool.name}_${span_condition.method}_${dataMatrix.name}" format="tabular"/>
		<data name="variableMetadata_out" label="${tool.name}_${span_condition.method}_${variableMetadata.name}" format="tabular"/>
		<data name="graph_output" label="${tool.name}_${span_condition.method}_graph" format="pdf"/>
		<data name="rdata_output" label="${tool.name}_${span_condition.method}_rdata" format="rdata"/>
	</outputs>

  <tests>
    <test>
      <param name="dataMatrix" value="input-batchcorrection-dataMatrix.tsv"/>
      <param name="sampleMetadata" value="input-batchcorrection-sampleMetadata.tsv"/>
      <param name="variableMetadata" value="input-batchcorrection-variableMetadata.tsv"/>
      <param name="method" value="all_loess_pool"/>
      <param name="span" value="1"/>
      <output name="dataMatrix_out" file="output-batchcorrection-dataMatrix.tsv"/>
    </test>
  </tests>
	
	
	<help>

.. class:: infomark

**Authors**
  | Jean-Francois Martin - PF MetaToul-AXIOM ; INRA ; MetaboHUB (for original version of this tool and overall development of the R script)
  | Melanie Petera - PFEM ; INRA ; MetaboHUB (for R wrapper and R script improvement)
  | Marion Landi - FLAME ; PFEM ; INRA ; MetaboHUB (for xml interface and R wrapper)
  | Franck Giacomoni - PFEM ; INRA ; MetaboHUB (for xml interface and R wrapper)
  | Etienne Thevenot - LIST/LADIS ; CEA ; MetaboHUB (for R script and wrapper regarding "all loess pool" and "all loess sample" methods)

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

.. class:: infomark

**Please cite** If you use this tool, please cite:

when using the **linear**, **lowess** or **loess** methods:
  | `F.M. Van Der Kloet, I. Bobeldijk, E.R. Verheij, R.H. Jellema. (2009). "Analytical error reduction using single point calibration for accurate and precise metabolomic phenotyping." Journal of Proteome Research p5132-5141 &lt;http://www.ncbi.nlm.nih.gov/pubmed/19754161&gt;`_

when using the **all loess pool** or **all loess sample** method:
  | `Dunn et al (2011). Procedures for large-scale metabolic profiling of serum and plasma using gas chromatography and liquid chromatography coupled to mass spectrometry. Nature Protocols, 6:1060-1083 &lt;http://dx.doi.org/10.1038/nprot.2011.335&gt;`_
  | Cleveland et al (1997). In Statistical Models in S; Chambers JM. and Hastie TJ. Ed.; Chapman et Hall: London; pp. 309-376
  | Etienne A. Thevenot, Aurelie Roux, Ying Xu, Eric Ezan, and Christophe Junot (2015). 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. *Journal of Proteome Research*, **14**:3322-3335 (http://dx.doi.org/10.1021/acs.jproteome.5b00354).

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

.. class:: infomark

**Tool updates**

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

================
Batch_correction
================

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

| **Instrumental drift** and **offset differences** between batches have been described in **LC-MS** experiments when the number of samples is large and/or multiple batches of acquisition are needed.
| Recently a normalization strategy relying on the measurements of a **pooled** (or QC) sample injected periodically has been described: for each variable, a **regression model** is fitted to the values of the **pool** and subsequently used to adjust the intensities of the samples of interest (van der Kloet et al, 2009; Dunn et al, 2011).
|
| The current tool implements **two strategies** which differ in the way the regression model is applied to the variables (either depending on variable quality metrics, or 'loess' model for all variables) and also in the generated figure.
|


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

.. image:: batch_correction.png
        :width: 800


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

+----------------------------+------------+
| Parameter : num + label    |   Format   |
+============================+============+
| 1 : Data Matrix file       |   tabular  |
+----------------------------+------------+
| 2 : Sample metadata file   |   tabular  |
+----------------------------+------------+
| 3 : Variable metadata file |   tabular  |
+----------------------------+------------+


Data Matrix file must contain the intensity values of variables.
	| First line must contain all the samples' names
	| First column must contain all the variables' ID
	| 

Sample metadata file must contain at least the three following columns: 
	| "batch" to identify the batches of analyses
	| "injectionOrder" (integers) defining the injection order of all samples (QC-pools as well as analysed samples)
	| "sampleType" indicating if a sample ("sample") or a QC-pool ("pool"); each batch needs
	| at least 3 QC-pools for intra-batch linear adjustment and 8 for lo(w)ess adjustment (5 for **all loess** methods)


.. class:: warningmark

MISSING DATA are allowed only with the **all loess** methods


----------
Parameters
----------

Type of regression model
	| To choose between *linear*, *lowess*, *loess*, *all loess pool*, and *all loess sample* strategies
	| **- Option 1** (**linear**, **lowess**, and **loess** methods): before the normalisation of each variable, some quality metrics are computed (see the "Determine Batch Correction" module); depending on the result, the variable can be normalized or not, with either the **linear**, **lowess** or **loess** model.
	| **- Option 2** (**all loess pool** and **all loess sample**): each variable is normalized by using the 'loess' model;
	| in the case **all loess pool** is chosen and the number of pool observations is below 5, the linear method is used (for all variables) and a warning is generated;
	| if the pool intensities are not representative of the samples (which can be viewed on the figure where both trends are shown), the case **all loess sample** enables using the sample intensities (instead of the pool intensities) as the reference for the loess curve.
	| In all "option 2" cases: the **median intensity of the reference observations** (either 'pool' or 'sample') is used as the scaling factor after the initial intensities have been divided by the loess predictions.
	|

Span
	| Smoothing parameter, advanced option for *lo(w)ess* and *all loess* methods
	| In case of a loess fit, the **span** parameter (between 0 and 1) controls the smoothing
	| (the higher the smoother; higher values are prefered to avoid overfitting; Cleveland et al, 1997).
	|

Null values
	| available for regression model *linear*, *lowess* and *loess*
	| Controls what is done regarding negative or infinite values that can be generated during regression estimation. 
	| *consider it as a missing value* will switch concerned intensities to NA;
	| this option implies that concerned ions will not be considered in PCA display. 
	| *consider it as a null intensity* will switch concerned intensities to 0 for lo(w)ess
	| or correct them by the batch mean instead of regression estimate for linear. 
	| 

Factor of interest
	| available for regression model *linear*, *lowess* and *loess*
	| Name of the factor (column header) in Sample metadata file that will be used as a categorical variable for plots and PCA.
	| (often a biological factor ; if none, leave "batch")
	| This factor does not affect correction calculation.
	| 

Level of details for plots
	| available for regression model *linear*, *lowess* and *loess*
	| *basic*: PCA + CV boxplot (before and after correction)
	| *standard*: 'basic' plots + before/after-correction plots of intensities over injection order, and design effects for each ion
	| *complete*: 'standard' plots + QC-pool regression plots per batch with samples' intensities over injection order
	| This factor is not used by the *all loess* methods where a unique figure is generated showing the sum of intensities along injection order, and the first 4 PCA scores.
	| 


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

Batch_correction_$method_rdata.rdata
	| binary data
	| Download, open R and use the 'load' function; objects are in the 'res' list
	|

Batch_correction_$method_graph.pdf
	| graphical output
	| For the *linear* and *lo(w)ess* methods, content depends on level of details chosen 
	|

Batch_correction_$method_variableMetadata.tabular
	| tsv output
	| Identical to the Variable metadata input file, with x more columns (where x is the number of batches) in case of *linear*, *lowess* and *loess* methods
	|

Batch_correction_$method_dataMatrix.tabular
	| tsv output (tabulated)
	| Same formatting as Data Matrix file; contains corrected intensities
	|

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

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

.. class:: infomark

Refer to the corresponding "W4M HowTo" page:
 | `MS data processing - Filters and normalisation &lt;http://workflow4metabolomics.org/sites/workflow4metabolomics.org/files/files/w4e-2016-data_processing.pdf&gt;`_
 |
 |

See also the reference history:
 | `W4M00001_Sacurine-statistics (DOI:10.15454/1.4811121736910142E12) &lt;http://dx.doi.org/10.15454/1.4811121736910142E12&gt;`_
 |

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

----
NEWS
----

CHANGES IN VERSION 2.1.2  
========================  

INTERNAL MODIFICATIONS  

Minor modifications in config file  

CHANGES IN VERSION 2.1.0
========================

INTERNAL MODIFICATIONS  

For PCA figure display only (**all_loess** options): missing values are set to the minimum value before PCA computation is performed (with svd)

Additional running and installation tests added with planemo, conda, and travis

BUG FIX

Variables with NA or 0 values in all reference samples are discarded before applying the **all_loess** normalization

INTERNAL MODIFICATIONS

Modifications of the **all_loess_wrapper** file to handle the recent **ropls** package versions (i.e. 1.3.15 and above) which use S4 classes

  </help>
      <!-- [RECOMMANDED] All citations associated to this tool (main citation given above and other references). Can be extracted from the history panel -->
    <citations>
        <!-- [HELP] As DOI or BibTex entry -->
        <citation type="doi">10.1021/pr900499r</citation>
        <citation type="doi">10.1038/nprot.2011.335</citation>
        <citation type="bibtex">@ARTICLE{Cleveland91,
            author = {Cleveland et al},
            year = {1991},
            journal = {Statistical Models in S, Chambers JM. and Hastie TJ. Ed., Chapman et Hall: London},
            title = {Local Regression Models},
            pages = {309-376},
            editor = {Chambers JM. and Hastie TJ. Ed.},
            publisher = {Chapman et Hall: London},
            chapter = {8}
        }</citation>
	<citation type="doi">10.1021/acs.jproteome.5b00354</citation>
    </citations>
	

</tool>