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planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
author melpetera
date Tue, 09 Aug 2016 06:47:41 -0400
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<tool id="Determine_BC" name="Determine_batch_correction" version="2.0.0">
  <description>to choose between linear, lowess and loess methods</description>

  <requirements>
    <requirement type="package" version="3.3.1">R</requirement>
    <requirement type="package">r-batch</requirement>
    <requirement type="package">r-ade4</requirement>
    <requirement type="package">r-pcaMethods</requirement>
  </requirements>

  <stdio>
    <exit_code range="1:" level="fatal" />
  </stdio>
 
  <command><![CDATA[
    Rscript $__tool_directory__/batch_correction_wrapper.R
      analyse "determine_bc"
      sampleMetadata "$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"
  ]]></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" />
    <param name="ref_factor" type="text" label="Factor of interest " help="column name of the factor of interest (often a biological factor); if none, leave 'batch'" value="batch" />
    <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="hide">
	  <param name="span" type="hidden" value="none"/>
	</when>	
        <when value="show">
          <param name="span" type="float" value="0.85" label="span" help="applied to lowess and loess regression"/>
        </when>
    </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** Franck Giacomoni and Marion Landi (for interface and wrapper) and Jean-Francois Martin and Melanie Petera (for R)

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

.. 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
-----------

| Allows to choose between linear or non-linear (lowess or loess) functions for batch correction
| using quality control pooled samples (QC-pools) with correction algorithm as mentioned 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 tools to help users to determine 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 make a choice in parameters,
| but it is not a requirement and thus can be avoided.


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

.. image:: ./static/images/metabolomics/determine_batch_correction.png
        :width: 800


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

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


Data Matrix file must contain the intensity values of the 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


.. class:: warningmark

NO MISSING DATA are allowed


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

Factor of interest
	| name of the factor (column header) that will be used as a categorical variable for plots.
	| (often a biological factor ; if none, leave “batch”).
	| 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 regression.


------------
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)
	| 3 : significant difference between QC-pools and samples means
	| 4 : denominator =0 when on 1 pool per batch non-0
	| 5 : (linear regression only) the slopes ratio “QC-pools/samples” is lower than -0.2
	|

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. 

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

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


.. class:: warningmark

Soon see the corresponding "Page"


</help>

<citations>
  <citation type="bibtex">@Article{Kloet2009,
  Title                    = {Analytical error reduction using single point calibration for accurate and precise metabolomic phenotyping},
  Author                   = {van der Kloet, Frans M. and Bobeldijk, Ivana and Verheij, Elwin R. and Jellema, Renger H.},
  Journal                  = {Journal of Proteome Research},
  Year                     = {2009},
  Note                     = {PMID: 19754161},
  Number                   = {11},
  Pages                    = {5132-5141},
  Volume                   = {8},

  Doi                      = {10.1021/pr900499r},
  Url                      = {http://pubs.acs.org/doi/abs/10.1021/pr900499r}
  }</citation>
  <citation type="doi">10.1093/bioinformatics/btu813</citation>
</citations>
  
<!--  
Input files
===========

| **These two input files can be used in the purview "URL/Text:" of the tool "Get Data/Upload File",**
| **by checking the box "Convert spaces to tabs: YES"**

Metadata_samples.txt
	Model input Sample metadata file::

		samples idLIMS serie factor01 factor02 batch injectionOrder sampleType
		POOL1 POOL1 pool p pool 01_08_2011 1 p
		X12588 12588 3 validation 2 01_08_2011 2 s
		X17736 17736 3 Q1 1 01_08_2011 3 s
		X15432 15432 3 validation 1 01_08_2011 4 s
		X17159 17159 3 Q4 1 01_08_2011 5 s
		X14325 14325 3 validation 2 01_08_2011 6 s
		X17419 17419 3 Q4 1 01_08_2011 7 s
		X16437 16437 3 Q4 1 01_08_2011 8 s
		X16172 16172 3 Q4 2 01_08_2011 9 s
		X16392 16392 3 Q4 2 01_08_2011 10 s
		X13875 13875 3 validation 2 01_08_2011 11 s
		POOL2 POOL2 pool p pool 01_08_2011 12 p
		X13117 13117 3 Q4 2 01_08_2011 13 s
		X13341 13341 3 Q1 2 01_08_2011 14 s
		X16888 16888 3 Q4 1 01_08_2011 15 s
		X17489 17489 3 Q4 2 01_08_2011 16 s
		X12718 12718 3 Q1 2 01_08_2011 17 s
		X16235 16235 3 Q4 2 01_08_2011 18 s
		X16878 16878 3 Q1 1 01_08_2011 19 s
		X12701 12701 3 validation 1 01_08_2011 20 s
		X16220 16220 3 Q4 2 01_08_2011 21 s
		X15635 15635 3 Q4 1 01_08_2011 22 s


Intensity_matrix.txt
	Model input Matrix Ions file BEFORE IMPLEMENTATION::

		samples POOL1 X12588 X17736 X15432 X17159 X14325 X17419 X16437 X16172 X16392 X13875 POOL2 X13117 X13341 X16888 X17489 X12718 X16235 X16878 X12701 X16220 X15635
		ion01 188.4140625 219.729126 122.5697632 123.5487671 805.8852539 183.4683838 37.33084106 151.8625488 97.12005615 91.24694824 69.87762451 195.4349365 112.4111938 136.7092285 159.9987793 172.1585693 0 117.5420532 133.6679688 80.05419922 160.0006104 760.0488281
		ion02 82.02575684 87.11358643 79.82391357 80.33862305 83.08575439 94.27703857 76.02288818 77.04394531 76.97564697 84.17669678 81.04943848 86.44024658 84.11865234 83.71282959 77.75219727 79.15936279 75.98492432 78.2835083 78.98760986 73.98388672 72.20550537 82.16448975
		ion03 25.31900024 24.2960968 23.29342651 31.54063416 30.3830719 22.42404175 35.44485474 26.38783264 17.1401825 21.27339172 20.25959778 26.33859253 18.17146301 26.32852173 24.30648804 28.34313965 29.37016296 18.23519897 24.48402405 25.38140869 24.35777283 21.31071472
		ion04 65.87536621 62.68716431 46.60232544 62.77856445 29.53218079 47.59136963 90.13983154 28.35336304 58.74325562 31.39331055 23.32928467 30.39666748 41.43960571 21.27049255 88.1161499 29.36820984 24.30200195 25.00007629 45.60662842 103.293457 37.46994019 87.09295654
		ion05 0 103.728544 279.5808214 884.2333448 824.5072072 434.6439081 764.82768 799.0972595 398.4002569 382.5370891 74.55342827 0 636.6596277 514.3863309 741.690017 412.3166491 660.8996555 57.36593795 102.2085264 455.6403091 548.6145486 515.8412195
		ion06 2711.785156 3465.292969 2469.75 3435.259766 2482.3125 2593.654297 1407.915039 1291.253906 2241.734375 1444.189453 3363.683594 2578.642578 2633.181641 3397.763672 3706.855469 3647.212891 3548.410156 3714.640625 1889.213867 2262.707031 2107.417969 2763.21875
		ion07 164.9023438 192.40625 140.7609863 192.4053955 139.7540283 140.748291 84.60144043 86.1819458 150.762207 89.90411377 207.5949707 164.0512695 149.8706055 186.336792 214.6140137 202.5360107 214.6877441 195.4482422 117.4679565 127.2941895 142.78479 163.0666504


Parameters
==========

Factor analysis  -> **batch**


Output files
============

out_preNormSummary.tabular:

====== ============== ==============
labion batch.1.linear batch.1.lowess
====== ============== ==============
ion01   2              2
ion02   2              2
ion03   2              2
ion04   2              2
ion05   1              1
...     ...            ...
====== ============== ==============


out_graph_pdf.pdf

.. image:: ./static/images/metabolomics/pdf_plotsituation.png
        :width: 800
-->

</tool>