annotate BC/determine_bc.xml @ 4:23314e1192d4 draft default tip

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<tool id="Determine_BC" name="Determine_batch_correction" version="3.0.0">
  <description>to choose between linear, lowess and loess methods</description>
  
  <macros>
    <import>macros.xml</import>
  </macros>
  
  <requirements>
    <requirement type="package" version="1.1_4">r-batch</requirement>
    <requirement type="package" version="1.7_8">r-ade4</requirement>
    <requirement type="package" version="1.70.0">bioconductor-pcamethods</requirement>
  </requirements>

  <stdio>
    <exit_code range="1:" level="fatal" />
  </stdio>
 
  <command><![CDATA[
    Rscript $__tool_directory__/batch_correction_3Lwrapper.R
      analyse "determine_bc"
      sampleMetadata "$sampleMetadata"
      dataMatrix "$dataMatrix"
      ref_factor "$ref_factor"
      #if str($advance.option ) == 'show':
        span $advance.span
      #else:
        span "none"
      #end if
      out_graph_pdf "$out_graph_pdf"
      out_preNormSummary "$out_preNormSummary"
      @SM_CUSTOM@
  ]]></command>
  
  <inputs>
    <param name="dataMatrix" type="data" label="Data matrix file " help="" format="tabular" />
    <param name="sampleMetadata" type="data" label="Sample metadata file " help="must contain at least the three following columns: 'batch' + 'injectionOrder' + 'sampleType'" format="tabular" />
    <expand macro="sm_customisation"/>
    <expand macro="foi"/>
    <conditional name="advance">
        <param name="option" type="select" label="Advanced options" help="should only be put at 'show' if you have good understanding of the span parameter and are willing to adjust it">
            <option value="show">show</option>
            <option value="hide" selected="true">hide</option>
        </param>
        <when value="show">
            <param name="span" type="float" value="0.85" label="span" help="applied to lowess and loess regression"/>
        </when>
        <when value="hide"/>
    </conditional>
  </inputs>
  
  <outputs>
    <data name="out_graph_pdf" label="Determine_BC_graph" format="pdf" ></data>
    <data name="out_preNormSummary" label="Determine_BC_preNormSummary" format="tabular" ></data>
  </outputs>

  <tests>
    <test>
      <param name="dataMatrix" value="input-determinebc-dataMatrix.tsv"/>
      <param name="sampleMetadata" value="input-determinebc-sampleMetadata.tsv"/>
      <param name="ref_factor" value="batch"/>
      <param name="option" value="hide"/>
      <param name="span" value="none"/>
      <output name="out_preNormSummary" file="output-determinebc-preNormSummary.txt"/>
    </test>
  </tests>

  <help>

.. class:: infomark

**Authors**
  | Jean-Francois Martin - PF MetaToul-AXIOM ; INRAE ; MetaboHUB (for original version of this tool and overall development of the R script)

.. class:: infomark

**Contributors**
  | Melanie Petera - PFEM ; INRAE ; MetaboHUB (for R wrapper and R script improvement)

.. class:: infomark

**Wrapping**
  | Marion Landi - FLAME ; PFEM (for original xml interface and R wrapper)
  | Franck Giacomoni - PFEM ; INRAE ; MetaboHUB (for original xml interface and R wrapper)

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

.. class:: infomark

**Please cite** If you use this tool, please cite:
  | `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;`_

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

==========================
Determine_batch_correction
==========================

| 

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

| 

Generates outputs to help to determine what type of regression to use between linear or non-linear (lowess or loess) functions for batch correction
using quality control pooled samples (QC-pools) with correction algorithm as described by Van Der Kloet (J Prot Res 2009).


Warning: this module does *not* deliver which choice should be made in model type;
it only provides information to help users in determining which choice may be appropriate, based on their own expertise.


This tool is meant to be used prior to the Batch_correction tool to help to make a choice in parameters,
but it is not a requirement and thus can be avoided.

| 

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

.. image:: determine_batch_correction.png
        :width: 600


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

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

| 

The 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.


The sample metadata file must contain at least the three following columns: 
 | - a batch column (default to "*batch*") to identify the batches of analyses
 | - an injection order column (default to "*injectionOrder*") composed of integers defining the injection order of samples
 | - a sample type column (default to "*sampleType*") indicating if a sample is a biological one ("*sample*"), a QC-pool ("*pool*") or a blank ("*blank*")
 | *Default values* can be changed according to your data coding using the customisation parameters in the "**Sample metadata file coding parameters**" section.


**Notes concerning your design:** 
 | - the 3 mandatory columns must not contain NA
 | - your data should contain at least 3 QC-pools in each batch for intra-batch **linear** adjustment and 8 for **lo(w)ess** adjustment



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

Sample metadata file coding parameters
 | Enables to give the names of columns in the sample metadata table that contain the injection order, the batches and the sample types.
 | Also enables to specify the sample type coding used in the sampletype column. 
 |

Factor of interest
 | Name of the factor (column header) that will be used as a categorical variable for design plots (often a biological factor ; if none, put the batch column name).
 | This factor does not affect correction calculation.
 |

Advanced options
 | Should only be put at "show" if you have good understanding of the span parameter and are willing to adjust it.
 |

Span
 | - When advanced option is at "hide" (default):
 | default is 1 for loess regression and is two times the ratio between number of pools and number of samples for lowess regression.
 | - When advanced option is at "show": 
 | filled value is used for lowess and loess regressions.


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

Determine_BC_preNormSummary.tabular
 | tabular output
 | Meaning of results of diagnosis analysis
 | 0 - no preliminary-condition problem
 | 1 - standard deviation of QC-pools or samples = 0
 | 2 - insufficient number of QC-pools within a batch (n=3 for linear, n=8 for lowess or loess)
 | 2.5 - less than 2 samples within a batch
 | 3 - significant difference between QC-pools' and samples' means
 | 4 - denominator =0 when on 1 pool per batch non-zero
 | 5 - (linear regression only) the slopes ratio “QC-pools/samples” is lower than -0.2
 | 6 - (linear regression only) none of the pool or sample could be corrected if negative and infinite values are turned into NA
 |

Determine_BC_graph.pdf
 | graphical output
 | One page per ion. Plots regression curves for all methods allowed and plot.design results regarding the factor of interest. 


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

----------------------
Additional information
----------------------


.. class:: warningmark

Refer to the corresponding "W4M HowTo" page:
 | `MS data processing - Filters and normalisation &lt;https://download.workflow4metabolomics.org/docs/w4e2018/2018-10_EC_W4E%20-%20Dataprocessing_Filter_and_normalisation.pdf&gt;`_
 |
 |


</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>
    </citations>
  


</tool>