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Merge pull request #627 from RECETOX/hechth/issue626
Added first set of bioconductor-msnbase tools
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| name: bioconductor-msnbase | ||
| owner: recetox | ||
| remote_repository_url: "https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-msnbase" | ||
| homepage_url: "https://bioconductor.org/packages/release/bioc/html/MSnbase.html" | ||
| categories: | ||
| - Metabolomics | ||
| - Proteomics | ||
| description: "MSnbase provides infrastructure for manipulation, processing and visualisation of mass spectrometry and proteomics data, ranging from raw to quantitative and annotated data. " | ||
| long_description: | | ||
| "MSnbase is an R/Bioconductor package that provides infrastructure for plotting, manipulation and processing mass spectrometry and proteomics data. | ||
| The project was started by Laurent Gatto in October 2010 (Mon Oct 4 23:35:23 2010, according to the git log) and has, since then, | ||
| benefited from various contributions, in particular Sebastian Gibb and Johannes Rainer. | ||
| The official package page is the Bioconductor landing page (release or devel versions). | ||
| The github page page is for active development, issue tracking and forking/pulling purposes." | ||
| auto_tool_repositories: | ||
| name_template: "{{ tool_id }}" | ||
| description_template: "{{ tool_name }} tool from the bioconductor-msnbase package" | ||
| suite: | ||
| name: suite_bioconductor_msnbase | ||
| description: MSnbase is an R/Bioconductor package that provides infrastructure for plotting, manipulation and processing mass spectrometry and proteomics data. | ||
| type: repository_suite_definition |
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tools/bioconductor-msnbase/bioconductor_msnbase_centroid.xml
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| <tool id="bioconductor_msnbase_centroid" name="bioconductor-msnbase centroid" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01" license="MIT"> | ||
| <description>centroid raw profile-mode MS data</description> | ||
| <macros> | ||
| <import>macros.xml</import> | ||
| </macros> | ||
| <expand macro="xrefs"/> | ||
| <expand macro="creator"/> | ||
| <expand macro="requirements"/> | ||
| <command detect_errors="exit_code"><![CDATA[ | ||
| Rscript "${run_script}" | ||
| ]]></command> | ||
| <configfiles> | ||
| <configfile name="run_script"><![CDATA[ | ||
| data_prof <- MSnbase::readMSData("$input_file", msLevel = $mslevel) | ||
| data_centroided <- MSnbase::pickPeaks( | ||
| data_prof, | ||
| halfWindowSize = ${halfWindowSize}, | ||
| method = "${estimate_noise_method}", | ||
| SNR = ${snr}, | ||
| refineMz = "${refinement.method}", | ||
| #if "$refinement.method" == "kNeighbors" | ||
| k = ${refinement.k} | ||
| #else if "$refinement.method" == "descendPeak" | ||
| signalPercentage = ${refinement.signal_percentage}, | ||
| stopAtTwo = ${refinement.stop_at_two} | ||
| #end if | ||
| ) | ||
| MSnbase::writeMSData( | ||
| data_centroided, | ||
| file = "centroided.mzml", | ||
| copy = TRUE, | ||
| outformat = "mzml" | ||
| ) | ||
| ]]></configfile> | ||
| </configfiles> | ||
| <inputs> | ||
| <param name="input_file" type="data" format="mzml" label="Input mzML File" | ||
| help="The input mzML file containing the mass spectrometry data to be centroided."/> | ||
| <param argument="mslevel" type="boolean" truevalue="2" falsevalue="1" checked="false" label="MS2" | ||
| help="Specify if the dataset contains MS2 (tandem mass spectrometry) data." /> | ||
| <param name="halfWindowSize" type="integer" label="Half window size" min="1" value="2" | ||
| help="The half window size for the centroiding method. This determines the number of data points on either side of the center point to include in the centroiding calculation."/> | ||
| <param name="estimate_noise_method" type="select" label="Noise estimation method" | ||
| help="Method to choose to estimate the noise in the spectrum."> | ||
| <option value="MAD" selected="true">Median Absolute Deviation</option> | ||
| <option value="SuperSmoother">Friedman's Super Smoother</option> | ||
| </param> | ||
| <param argument="--snr" type="float" min="0" value="3" label="Signal-to-noise ratio (SNR)" | ||
| help="The signal-to-noise ratio threshold for removing noisy signals." /> | ||
| <conditional name="refinement"> | ||
| <param name="method" type="select" label="Peak refinement method" | ||
| help="The method refines the m/z value of the identified centroids by considering data points that belong (most likely) to the same mass peak. | ||
| The m/z value is calculated as an intensity weighted average of the m/z values within the peak region. | ||
| How the peak region is defined depends on the method chosen."> | ||
| <option value="none" selected="true">None</option> | ||
| <option value="kNeighbors">K-Neighbors</option> | ||
| <option value="descendPeak">Descend Peak</option> | ||
| </param> | ||
| <when value="kNeighbors"> | ||
| <param argument="--k" type="integer" min="1" max="10" value="2" label="K" | ||
| help="The number of 2*K nearest neighbors to consider for m/z interpolation during peak refinement."/> | ||
| </when> | ||
| <when value="descendPeak"> | ||
| <param argument="--signal_percentage" type="integer" min="0" max="100" value="20" label="Intensity threshold (%)" | ||
| help="The signal intensity cutoff threshold (as a percentage) for including values in the m/z calculation during peak refinement." /> | ||
| <param argument="stop_at_two" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Stop at two" | ||
| help="Specify whether to stop the descent only after encountering two increasing scans, instead of stopping at the first increasing scan." /> | ||
| </when> | ||
| <when value="none"/> | ||
| </conditional> | ||
| </inputs> | ||
| <outputs> | ||
| <data name="output_file" format="mzml" label="${on_string} centroided with refinement ${refinement.method}" from_work_dir="centroided.mzml"/> | ||
| </outputs> | ||
| <tests> | ||
| <test> | ||
| <param name="input_file" value="29_qc_no_dil_milliq_subset.mzML"/> | ||
| <output name="output_file"> | ||
| <assert_contents> | ||
| <expand macro="assertions_centroiding"/> | ||
| </assert_contents> | ||
| </output> | ||
| </test> | ||
| <test> | ||
| <param name="input_file" value="29_qc_no_dil_milliq_subset.mzML"/> | ||
| <param name="method" value="kNeighbors"/> | ||
| <param name="k" value="3"/> | ||
| <output name="output_file"> | ||
| <assert_contents> | ||
| <expand macro="assertions_centroiding"/> | ||
| </assert_contents> | ||
| </output> | ||
| </test> | ||
| <test> | ||
| <param name="input_file" value="29_qc_no_dil_milliq_subset.mzML"/> | ||
| <param name="method" value="descendPeak"/> | ||
| <param name="signal_percentage" value="10"/> | ||
| <output name="output_file"> | ||
| <assert_contents> | ||
| <expand macro="assertions_centroiding"/> | ||
| </assert_contents> | ||
| </output> | ||
| </test> | ||
| </tests> | ||
| <help><![CDATA[ | ||
| .. class:: infomark | ||
| **What it does** | ||
| This tool performs centroiding on mass spectrometry data using the MSnbase package in R. Centroiding is a process that converts profile mode data to centroid mode by identifying the peaks in the mass spectrum and representing them as single points. | ||
| **Usage** | ||
| - **Input**: Provide the input mzML file containing the mass spectrometry data to be centroided. | ||
| - **Parameters**: | ||
| - **Input mzML File**: The input mzML file containing the mass spectrometry data to be centroided. | ||
| - **MS2**: Specify if the dataset contains MS2 (tandem mass spectrometry) data. | ||
| - **Half window size**: The number of data points on either side of the center point to include in the centroiding calculation. | ||
| - **Noise estimation method**: Choose the method to estimate the noise in the spectrum. Options include Median Absolute Deviation (MAD) and Friedman's Super Smoother. | ||
| - **Signal-to-noise ratio (SNR)**: The signal-to-noise ratio threshold for removing noisy signals. A higher value will result in more noise being filtered out. | ||
| - **Peak refinement method**: Select the method to refine the m/z value of the identified centroids. Options include None, K-Neighbors, and Descend Peak. | ||
| - **K**: The number of 2*K nearest neighbors to consider for m/z interpolation during peak refinement (only applicable if K-Neighbors method is selected). | ||
| - **Intensity threshold (%)**: The signal intensity cutoff threshold (as a percentage) for including values in the m/z calculation during peak refinement (only applicable if Descend Peak method is selected). | ||
| - **Stop at two**: Specify whether to stop the descent only after encountering two increasing scans, instead of stopping at the first increasing scan (only applicable if Descend Peak method is selected). | ||
| - **Output**: The centroided mzML file. | ||
| **Input** | ||
| - **Input mzML File**: The input mzML file containing the mass spectrometry data to be centroided. | ||
| **Output** | ||
| - **Output mzML File**: The resulting mzML file after applying the centroiding algorithm. | ||
| **References** | ||
| For more detailed information, please refer to the original documentation available via Bioconductor: https://bioconductor.org/packages/release/bioc/html/MSnbase.html | ||
| ]]></help> | ||
| <expand macro="citations"/> | ||
| </tool> |
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tools/bioconductor-msnbase/bioconductor_msnbase_smooth_chromatogram.xml
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| <tool id="bioconductor_msnbase_smooth_chromatogram" name="bioconductor-msnbase smooth chromatogram" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01" license="MIT"> | ||
| <description>smooth consecutive spectra using a moving window filter (combineSpectraMovingWindow)</description> | ||
| <macros> | ||
| <import>macros.xml</import> | ||
| </macros> | ||
| <edam_topics> | ||
| <edam_topic>topic_3170</edam_topic> <!-- Proteomics --> | ||
| <edam_topic>topic_3391</edam_topic> <!-- Data handling --> | ||
| </edam_topics> | ||
| <edam_operations> | ||
| <edam_operation>operation_3632</edam_operation> <!-- Data smoothing --> | ||
| <edam_operation>operation_2945</edam_operation> <!-- Data handling --> | ||
| </edam_operations> | ||
|
|
||
| <expand macro="xrefs"/> | ||
| <expand macro="creator"/> | ||
| <expand macro="requirements"/> | ||
|
|
||
| <command detect_errors="exit_code"><![CDATA[ | ||
| Rscript "${run_script}" | ||
| ]]></command> | ||
| <configfiles> | ||
| <configfile name="run_script"><![CDATA[ | ||
| data_prof <- MSnbase::readMSData("$input_file", mode = "onDisk") | ||
| data_smoothed <- MSnbase::combineSpectraMovingWindow( | ||
| data_prof, | ||
| halfWindowSize = ${halfWindowSize}, | ||
| intensityFun = ${intensity_function}, | ||
| mzd = 0, | ||
| timeDomain = $qtof, | ||
| weighted = $weighted, | ||
| ppm = $ppm, | ||
| BPPARAM = BiocParallel::bpparam() | ||
| ) | ||
| MSnbase::writeMSData( | ||
| data_smoothed, | ||
| file = "smoothed.mzml", | ||
| copy = TRUE, | ||
| outformat = "mzml" | ||
| ) | ||
| ]]></configfile> | ||
| </configfiles> | ||
| <inputs> | ||
| <param name="input_file" type="data" format="mzml" label="Input mzML File" help="The input mzML file containing the MSnbase data."/> | ||
| <param name="halfWindowSize" type="integer" label="Half window size" min="2" value="4" | ||
| help="The half window size for the moving window smoothing method. This determines the number of data points on either side of the center point to include in the smoothing calculation."/> | ||
| <param name="weighted" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Weighted" | ||
| help="Specify whether to apply a weighted moving average, where the weights depend on the distance from the center of the window." /> | ||
| <param name="qtof" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="QTOF" | ||
| help="Indicate if the data was acquired using a QTOF (Quadrupole Time-of-Flight) instrument, which affects the time domain processing." /> | ||
| <param argument="--ppm" type="integer" min="0" value="3" label="ppm tolerance" | ||
| help="The parts-per-million (ppm) tolerance for considering mz values as belonging to the same ion. A higher value allows for more variation in mz values." /> | ||
| <param name="intensity_function" type="select" label="Function to combine intensities" | ||
| help="Choose the function to combine the intensity values of the same m/z value within the moving window. Options include mean, median, min, max, and sum."> | ||
| <option value="base::mean" selected="true">mean</option> | ||
| <option value="stats::median">median</option> | ||
| <option value="min">min</option> | ||
| <option value="max">max</option> | ||
| <option value="sum">sum</option> | ||
| </param> | ||
| </inputs> | ||
| <outputs> | ||
| <data name="output_file" format="mzml" label="Chromatogram smoothing on ${on_string}" from_work_dir="smoothed.mzml"/> | ||
| </outputs> | ||
| <tests> | ||
| <test> | ||
| <param name="input_file" value="29_qc_no_dil_milliq_subset.mzML"/> | ||
| <output name="output_file"> | ||
| <assert_contents> | ||
| <expand macro="assertions_smoothing"/> | ||
| <has_size size="173532" delta="100"/> | ||
| </assert_contents> | ||
| </output> | ||
| </test> | ||
| </tests> | ||
| <help><![CDATA[ | ||
| .. class:: infomark | ||
| **What it does** | ||
| This tool performs chromatogram smoothing on mass spectrometry data using the MSnbase package in R. It applies a moving window smoothing method to the input mzML file, which helps in reducing noise and improving the signal quality. | ||
| **Usage** | ||
| - **Input**: Provide the input mzML file containing the mass spectrometry data to be smoothed. | ||
| - **Parameters**: | ||
| - **Half window size**: The number of data points on either side of the center point to include in the smoothing calculation. | ||
| - **Weighted**: Whether to apply a weighted moving average. | ||
| - **QTOF**: Indicate if the data was acquired using a QTOF instrument. | ||
| - **ppm tolerance**: The parts-per-million tolerance for considering mz values as belonging to the same ion. | ||
| - **Function to combine intensities**: Choose the function to combine the intensity values within the moving window. | ||
| - **Output**: The smoothed mzML file. | ||
| **Input** | ||
| - **Input mzML File**: The input mzML file containing the MSnbase data to be smoothed. | ||
| **Output** | ||
| - **Output mzML File**: The resulting mzML file after applying the smoothing algorithm. | ||
| ]]></help> | ||
| <expand macro="citations"/> | ||
| </tool> |
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