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author | marie-tremblay-metatoul |
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date | Thu, 24 Nov 2016 12:11:04 -0500 |
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<tool id="NmrAlignment" name="NMR_Alignment" version="2016-10-07"> <description> Alignment of NMR spectra based on the Cluster-based Peak Alignment (CluPA) algorithm </description> <requirements> <requirement type="package" version="3.1.2">R</requirement> <requirement type="package" version="1.1_4">r-batch</requirement> <requirement type="package" version="1.2.1">r-speaq</requirement> </requirements> <stdio> <exit_code range="1:" level="fatal" /> </stdio> <command> ## Wrapper Rscript $__tool_directory__/NmrAlignment_wrapper.R ## File input #if $inputs.input == "lib": library $__app__.config.user_library_import_dir/$__user_email__/$inputs.library #elif $inputs.input == "zip_file": zipfile $inputs.zip_file #end if ## Spectra borders left_border $left_border right_border $right_border ## Exclusion zone zone_exclusion_choices.choice ${zone_exclusion_choices.choice} #if str($zone_exclusion_choices.choice) == 'yes': #for $i in $zone_exclusion_choices.conditions: zone_exclusion_left ${i.zone_exclusion_left} zone_exclusion_right ${i.zone_exclusion_right} #end for #end if ## Reference spectrum reference $reference ## Segment size nDivRange $nDivRange ## Intensity threshold baselineThresh $baselineThresh ## Outputs logOut $logOut alignedSpectra $alignedSpectra graphOut $graphOut </command> <inputs> <conditional name="inputs"> <param name="input" type="select" label="Choose your inputs method" > <option value="zip_file" selected="true">Zip file from your history containing your Bruker directories</option> <option value="lib" >Library directory name</option> </param> <when value="zip_file"> <param name="zip_file" type="data" format="no_unzip.zip" label="Zip file" /> </when> <when value="lib"> <param name="library" type="text" size="40" label="Library directory name" help="The name of your directory containing all your data" > <validator type="empty_field"/> </param> </when> </conditional> <param name="left_border" label="Left Border" type="float" value="10.0" size="10" help="Default value is 10 ppm"/> <param name="right_border" label="Right Border" type="float" value="0.5" size="10" help="Default value is 0.5 ppm"/> <conditional name="zone_exclusion_choices"> <param name="choice" type="select" label="Exclusion zone(s)" help="Choose if you want to exclude particular zone(s)" > <option value="yes" > yes </option> <option value="no" selected="true"> no </option> </param> <when value="yes"> <repeat name="conditions" title="exclusion zones"> <param name="zone_exclusion_left" label="Left exclusion zone border" type="float" value="10.0" /> <param name="zone_exclusion_right" label="Right exclusion zone border" type="float" value="10.0" /> </repeat> </when> <when value="no" /> </conditional> <param name="reference" type="integer" value="0" help="Number of the reference spectrum. Default value is 0: automatic determination of the reference spectrum" /> <param name="nDivRange" type="integer" value="64" help="Size of a single small segment after division of spectra. Default value is 64" /> <param name="baselineThresh" type="integer" value="1" help="Threshold to remove all peaks with intensity lower this value. Default value is 1" /> </inputs> <outputs> <data format="txt" name="logOut" label="${tool.name}_log" /> <data format="tabular" name="alignedSpectra" label="${tool.name}_alignedSpectra" /> <data format="pdf" name="graphOut" label="${tool.name}_graph" /> </outputs> <help> .. class:: infomark **Authors** Marie Tremblay-Franco (marie.tremblay-franco@toulouse.inra.fr) .. class:: infomark **Please cite** T.N. Vu, D. Valkenborg, K. Smets, K.A. Verwaest, R. Dommisse, F. Lemière, A. Verschoren, B. Goethals and K. Laukens. An integrated workflow for robust alignment and simplified quantitative analysis of NMR spectrometry data. BMC Bioinformatics 2011, 12:405. DOI: 10.1186/1471-2105-12-405 T.N. Vu, K. Laukens and D. Valkenborg. A practical experiment of using speaq package. 2015 (https://cran.r-project.org/web/packages/speaq/vignettes/speaq.pdf) ============= NMR Alignment ============= ----------- Description ----------- Nuclear Magnetic Resonance Spectrum Alignment based on the Cluster-based Peak Alignment (CluPA) algorithm from the R 'speak' package ----------------- Workflow position ----------------- **Upstream tools** ========================= ================= ======= Name output file format ========================= ================= ======= NA NA NA ========================= ================= ======= **Downstream tools** +---------------------------+----------------------+--------+ | Name | Output file | Format | +===========================+======================+========+ |NmrBucketing | dataMatrix.tsv | Tabular| +---------------------------+----------------------+--------+ | | sampleMetadata.tsv | Tabular| +---------------------------+----------------------+--------+ | | variableMetadata.tsv | Tabular| +---------------------------+----------------------+--------+ |NmrNormalization | dataMatrix.tsv | Tabular| +---------------------------+----------------------+--------+ | | sampleMetadata.tsv | Tabular| +---------------------------+----------------------+--------+ | | variableMetadata.tsv | Tabular| +---------------------------+----------------------+--------+ |Univariate | variableMetadata.tsv | Tabular| +---------------------------+----------------------+--------+ |Multivariate | sampleMetadata.tsv | Tabular| +---------------------------+----------------------+--------+ | | variableMetadata.tsv | Tabular| +---------------------------+----------------------+--------+ ----------- Input files ----------- +---------------------------+------------+ | Parameter : num + label | Format | +===========================+============+ | 1 : Choose your inputs | zip | +---------------------------+------------+ **Choose your inputs** | Zip file (recommended): You can put a zip file containing your inputs: myinputs.zip (containing all your conditions as sub-directories). ---------- Parameters ---------- Bucket width | size of windows | Left limit | Upper boundary: values greater than this value are not used in the bucketing. Default value is 10.0 ppm | Right limit | Lower boundary: values lower than this value are not used in the bucketing. Default value is 0.5 ppm | Exclusion zone(s) | Spectral regions to exclude, water, solvents, ... resonance | If YES: parameters **Lower exclusion zone** and **Upper exclusion zone** are visible, | If NO: no zone to exclude | Default value is NO | Left exclusion zone | Upper boundary of exclusion zone | Right exclusion zone | Lower boundary of exclusion zone | *Notes:* | - these parameters can be used several times using the "Add new exclusion zones" button | Reference spectrum | spectrum to which other spectra are aligned | Default value is 0: heuristic strategy to find the optimal template developped in the speaq package | Segment size | Size of a single small segment after division of spectra | Default value: 64 (minimal value adviced) | Intensity threshold | All peaks with an intensity below this threshold are removed | Default value: 1 | ------------ Output files ------------ alignedSpectra.tsv | tabular output | Data matrix with p rows (ppm) and n columns (samples) containing the aligned intensities | graphOut.pdf | pdf output | Graphical chart of raw and aligned data: whole spectral width, "zoomed" zones depending on the exclusion zones, spectral zone between 2.8 and 2.4ppm corresponding to the citric acid --------------------------------------------------- --------------- Example --------------- .. image:: ./static/images/NmrAlignment.png :width: 500 </help> <citations> <citation type="doi">10.1093/bioinformatics/btu813</citation> </citations> </tool>