Mercurial > repos > marie-tremblay-metatoul > spectral_normalization
diff NmrNormalization_xml.xml @ 0:a5e6499f1b4d draft default tip
planemo upload for repository https://github.com/workflow4metabolomics/spectral_normalization commit 559844c168f0450b9657346ba890d9c028d7537a
| author | marie-tremblay-metatoul |
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| date | Tue, 22 Nov 2016 06:42:44 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NmrNormalization_xml.xml Tue Nov 22 06:42:44 2016 -0500 @@ -0,0 +1,277 @@ +<tool id="spectral_normalization" name="Spectral Normalization" version="1.0.2"> + + <description> Normalization of (preprocessed) spectra </description> + + <requirements> + <requirement type="package" version="1.1_4">r-batch</requirement> + </requirements> + + <stdio> + <exit_code range="1:" level="fatal" /> + </stdio> + + <command> + 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 + sampleMetadataOut $sampleMetadataOut + variableMetadataOut $variableMetadataOut + graphOut $graphOut + + + </command> + + <inputs> + <param name="dataMatrix" type="data" label="Data matrix of spectral data" help="" format="tabular" /> + + <conditional name="scalingMethod" > + <param name="method" label="Normalization method" type="select" help="Default method is total intensity" > + <option value="None">None normalization</option> + <option value="Total">Total intensity</option> + <option value="PQN">Probabilistic Quotient Normalization</option> + <option value="QuantitativeVariable">Quantitative variable</option> + </param> + <when value="None" /> + <when value="Total" /> + <when value="PQN"> + <param name="sampleMetadata" type="data" label="Sample metadata matrix" help="" format="tabular" /> + <param name="factor" label="Name of the column of the biological factor of interest (for PQN method)" type="text" /> + <param name="controlGroup" label="Name of reference level for PQN normalization" type="text" help=""/> + </when> + <when value="QuantitativeVariable"> + <param name="sampleMetadata" type="data" label="Sample metadata matrix" help="" format="tabular" /> + <param name="factor" label="Name of the column of the numerical variable for normalization (weight, osmolality, ...)" type="text" /> + </when> + </conditional> + + <param name="graphType" label="Spectra representation" type="select" help="Select 'None' for no representation,'Overlay' to overlay all spectra on a unique chart and 'One per individual' to generate an individual chart for each observation"> + <option value="None"> none </option> + <option value="Overlay"> Overlay </option> + <option value="One_per_individual"> One_per_individual </option> + </param> + </inputs> + + + <outputs> + <data format="txt" name="logOut" label="${tool.name}_log" /> + <data format="tabular" name="sampleMetadataOut" label="${tool.name}_sampleMetadata" /> + <data format="tabular" name="variableMetadataOut" label="${tool.name}_variableMetadata" /> + <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> + <param name="dataMatrix" value="MTBLS1_bucketedData.tabular" ftype="tabular" /> + <param name="scalingMethod|method" value="Total" /> + <param name="graphType" value="Overlay" /> + <output name="dataMatrixOut" file="MTBLS1_bucketedData_normalized.tabular" /> + <output name="sampleMetadataOut" file="MTBLS1_sampleMetadata_normalized.tabular" /> + <output name="variableMetadataOut" file="MTBLS1_variableMetadata_normalized.tabular" /> + </test> + </tests> + + <help> + +.. class:: infomark + +**Authors** Marie Tremblay-Franco (marie.tremblay-franco@toulouse.inra.fr) and Marion Landi (marion.landi@clermont.inra.fr) + MetaboHUB: The French National Infrastructure for Metabolomics and Fluxomics (http://www.metabohub.fr/en) + +--------------------------------------------------- + +.. 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. + +--------------------------------------------------- + +====================== +Spectral Normalization +====================== + +----------- +Description +----------- + +Normalization (operation applied on each (preprocessed) individual spectrum) of spectral 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 (buckets) and n columns (samples) containing the intensities + | + +sampleMetadata.tsv + | tabular output + | sampleMetadata file identical to the file given as argument if "PQN" or "Quantitative" normalization method; file with n rows (samples) and 2 columns containing sample identifier (rownames) and sample order if "None" or "Total" normalization methof + | Mandatory file in the statistical analysis step of the workflow + | + +variableMetadata.tsv + | tabular output + | file with p rows (buckets) and 2 columns containing variable identifier (rownames) and bucket order. Can add columns with numeric and/or character variable metadata. + | Mandatory file in the statistical analysis step of the workflow + | + +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 1.0.2 - 22/10/2016** + +- NEW: this tool was previously named NMR Normalization. It had been generalize to deal with all kind of spectral 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>