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NmrNormalization_xml.xml
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<tool id="normalization" name="Normalization" version="1.0.7+galaxy2">
<description> Normalization of (preprocessed) spectra </description>
<requirements>
<requirement type="package" version="1.1_4">r-batch</requirement>
</requirements>
<required_files>
<include path="NmrNormalization_wrapper.R" />
<include path="NmrNormalization_script.R" />
<include path="DrawSpec.R" />
</required_files>
<stdio>
<exit_code range="1:" level="fatal" />
</stdio>
<command><![CDATA[
Rscript $__tool_directory__/NmrNormalization_wrapper.R
## Data matrix of bucketed and integrated spectra
dataMatrix $dataMatrix
## Normalization method
scalingMethod $scalingMethod.method
#if $scalingMethod.method == "PQN":
## Sample metadata matrix
sampleMetadata $scalingMethod.sampleMetadata
## Biological factor of interest (column number in samplemetadata)
factor $scalingMethod.factor
## Reference class
controlGroup $scalingMethod.controlGroup
#end if
#if $scalingMethod.method == "QuantitativeVariable":
## Sample metadata matrix
sampleMetadata $scalingMethod.sampleMetadata
## Biological factor of interest (column number in samplemetadata)
factor $scalingMethod.factor
#end if
## Spectra representation
graphType $graphType
## Outputs
logOut $logOut
dataMatrixOut $dataMatrixOut
graphOut $graphOut
]]></command>
<inputs>
<param name="dataMatrix" type="data" label="Data matrix of preprocessed data" help="" format="tabular" />
<conditional name="scalingMethod" >
<param name="method" label="Normalization method" type="select" help="Default method is total intensity" >
<option value="None">None normalization</option>
<option value="Total">Total intensity</option>
<option value="PQN">Probabilistic Quotient Normalization</option>
<option value="QuantitativeVariable">Quantitative variable</option>
</param>
<when value="None" />
<when value="Total" />
<when value="PQN">
<param name="sampleMetadata" type="data" label="Sample metadata matrix" help="" format="tabular" />
<param name="factor" label="Name of the column of the biological factor of interest (for PQN method)" type="text" />
<param name="controlGroup" label="Name of reference level for PQN normalization" type="text" help=""/>
</when>
<when value="QuantitativeVariable">
<param name="sampleMetadata" type="data" label="Sample metadata matrix" help="" format="tabular" />
<param name="factor" label="Name of the column of the numerical variable for normalization (weight, osmolality, ...)" type="text" />
</when>
</conditional>
<param name="graphType" label="Spectra representation" type="select" help="Select 'None' for no representation,'Overlay' to overlay all spectra on a unique chart and 'One per individual' to generate an individual chart for each observation">
<option value="None"> none </option>
<option value="Overlay"> Overlay </option>
<option value="One_per_individual"> One_per_individual </option>
</param>
</inputs>
<outputs>
<data format="txt" name="logOut" label="${tool.name}_log" />
<data format="tabular" name="dataMatrixOut" label="${tool.name}_dataMatrix" />
<data format="pdf" name="graphOut" label="${tool.name}_spectra" >
<filter> graphType != "None" </filter>
</data>
</outputs>
<tests>
<test expect_num_outputs="3">
<param name="dataMatrix" value="MTBLS1_bucketedData.tabular.tsv" ftype="tabular" />
<conditional name="scalingMethod" >
<param name="method" value="Total" />
</conditional>
<param name="graphType" value="Overlay" />
<output name="dataMatrixOut" file="MTBLS1_bucketedData_normalized.tabular" />
</test>
</tests>
<help>
.. class:: infomark
**Authors** Marie Tremblay-Franco ([email protected]) and Marion Landi ([email protected])
MetaboHUB: The French National Infrastructure for Metabolomics and Fluxomics (https://www.metabohub.fr/home.html)
---------------------------------------------------
.. class:: infomark
**Please cite**
F. Dieterle, A. Ross, G. Schlotterbeck, and H. Senn (2006). Probabilistic Quotient Normalization as Robust Method to Account for Dilution of Complex Biological Mixtures. Application in 1H NMR Metabonomics.
Analytical Chemistry 78(13): 4281-4290.
---------------------------------------------------
===============
Normalization
===============
-----------
Description
-----------
Normalization (operation applied on each (preprocessed) individual spectrum) of preprocessed data
-----------------
Workflow position
-----------------
**Upstream tools**
+----------------------+------------------------------------+---------+-------------+
| Name | output file | format | parameter |
+======================+====================================+=========+=============+
| NMR_Bucketing | Normalization_bucketedData.tsv | tabular | Ions Matrix |
+----------------------+------------------------------------+---------+-------------+
**Downstream tools**
+---------------------------+----------------------+--------+
| Name | Output file | Format |
+===========================+======================+========+
|Univariate | variableMetadata.tsv | Tabular|
+---------------------------+----------------------+--------+
|Multivariate | sampleMetadata.tsv | Tabular|
+---------------------------+----------------------+--------+
| | variableMetadata.tsv | Tabular|
+---------------------------+----------------------+--------+
-----------
Input files
-----------
+---------------------------+------------+
| Parameter : num + label | Format |
+===========================+============+
| DataMatrix | Tabular |
+---------------------------+------------+
**DataMAtrix**
| variable x sample dataMatrix tabular separated file containing (preprocessed) spectra, with . as decimal, and NA for missing values
----------
Parameters
----------
DataMatrix
| see "Input files" section above
|
Normalization method
| normalization to apply on each spectrum:
+---------------------------+--------------------------------------+
| Name | Normalization |
+===========================+======================================+
|None | No |
+---------------------------+--------------------------------------+
|Total | Total intensity |
+---------------------------+--------------------------------------+
|PQN | Probabilistic Quotient Normalization |
+---------------------------+--------------------------------------+
|QuantitativeVariable | Weight, osmolality, ... |
+---------------------------+--------------------------------------+
sampleMetadata
| sample x metadata **sample** tabular separated file of the numeric and/or character sample metadata, with . as decimal and NA for missing values
| Mandatory for "PQN" or "Quantitative" normalization method
| The row names must be identical to the column names of the dataMatrix file
|
Spectra representation:
| Graphical chart of bucketed and integrated raw files
| If "Overlay": the n (sample number) spectra are overlaid on the same figure
| If "One_per_individual": pdf file includes n pages (1 per sample)
|
------------
Output files
------------
dataMatrix.tsv
| tabular output
| Data matrix with p rows (variable) and n columns (samples) containing the intensities
|
spectra.pdf
| pdf output
| Graphical chart of bucketed and integrated data
|
---------------------------------------------------
---------------
Working example
---------------
.. class:: warningmark
Under construction
.. image:: ./static/images/Mth_Travaux.png
:width: 100
---------------------------------------------------
--------------
Changelog/News
--------------
**Version 1.0.7 - 25/09/2018**
- Bug fixing for PQN normalization in case of zero's
**Version 1.0.3 - 30/01/2017**
- BUGFIX: Fix a bug: stack overflow for integers
**Version 1.0.2 - 22/10/2016**
- NEW: this tool was previously named NMR Normalization. It had been generalize to deal with all kind of preprocessed data
**Version 1.0.1 - 14/04/2016**
- TEST: refactoring to pass planemo test using conda dependencies
**Version 2015-01-28 - 28/01/2015**
</help>
<citations>
<citation type="doi">10.1093/bioinformatics/btu813</citation>
</citations>
</tool>