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Commit message:
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-msnbase commit 8a94b9932a94c323a33dfe858ee0a2c57fb04701 |
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added:
bioconductor_msnbase_centroid.xml macros.xml test-data/29_qc_no_dil_milliq_subset.mzML |
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| diff -r 000000000000 -r 4018639dc0a5 bioconductor_msnbase_centroid.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bioconductor_msnbase_centroid.xml Fri Jan 24 15:58:07 2025 +0000 |
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| b'@@ -0,0 +1,142 @@\n+<tool id="bioconductor_msnbase_centroid" name="bioconductor-msnbase centroid" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01" license="MIT">\n+ <description>centroid raw profile-mode MS data</description>\n+ <macros>\n+ <import>macros.xml</import>\n+ </macros>\n+ <expand macro="xrefs"/>\n+ <expand macro="creator"/>\n+ <expand macro="requirements"/>\n+ <command detect_errors="exit_code"><![CDATA[\n+ Rscript "${run_script}"\n+ ]]></command>\n+ <configfiles>\n+ <configfile name="run_script"><![CDATA[\n+ data_prof <- MSnbase::readMSData("$input_file", msLevel = $mslevel)\n+\n+ data_centroided <- MSnbase::pickPeaks(\n+ data_prof,\n+ halfWindowSize = ${halfWindowSize},\n+ method = "${estimate_noise_method}",\n+ SNR = ${snr},\n+ refineMz = "${refinement.method}",\n+ #if "$refinement.method" == "kNeighbors"\n+ k = ${refinement.k}\n+ #else if "$refinement.method" == "descendPeak"\n+ signalPercentage = ${refinement.signal_percentage},\n+ stopAtTwo = ${refinement.stop_at_two}\n+ #end if\n+ )\n+\n+ MSnbase::writeMSData(\n+ data_centroided,\n+ file = "centroided.mzml",\n+ copy = TRUE,\n+ outformat = "mzml"\n+ )\n+ ]]></configfile>\n+ </configfiles>\n+ <inputs>\n+ <param name="input_file" type="data" format="mzml" label="Input mzML File"\n+ help="The input mzML file containing the mass spectrometry data to be centroided."/>\n+ <param argument="mslevel" type="boolean" truevalue="2" falsevalue="1" checked="false" label="MS2"\n+ help="Specify if the dataset contains MS2 (tandem mass spectrometry) data." />\n+ <param name="halfWindowSize" type="integer" label="Half window size" min="1" value="2"\n+ 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."/>\n+ <param name="estimate_noise_method" type="select" label="Noise estimation method"\n+ help="Method to choose to estimate the noise in the spectrum.">\n+ <option value="MAD" selected="true">Median Absolute Deviation</option>\n+ <option value="SuperSmoother">Friedman\'s Super Smoother</option>\n+ </param>\n+ <param argument="--snr" type="float" min="0" value="3" label="Signal-to-noise ratio (SNR)"\n+ help="The signal-to-noise ratio threshold for removing noisy signals." />\n+ <conditional name="refinement">\n+ <param name="method" type="select" label="Peak refinement method" \n+ 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.\n+ The m/z value is calculated as an intensity weighted average of the m/z values within the peak region.\n+ How the peak region is defined depends on the method chosen.">\n+ <option value="none" selected="true">None</option>\n+ <option value="kNeighbors">K-Neighbors</option>\n+ <option value="descendPeak">Descend Peak</option>\n+ </param>\n+ <when value="kNeighbors">\n+ <param argument="--k" type="integer" min="1" max="10" value="2" label="K"\n+ help="The number of 2*K nearest neighbors to consider for m/z interpolation during peak refinement."/>\n+ </when>\n+ <when value="descendPeak">\n+ <param argument="--signal_percentage" type="integer" min="0" max="100" value="20" label="Intensity threshold (%)"\n+ help="The signal intensity cutoff threshold (as a percentage) for including values in the m/z calculation during peak ref'..b' help="Specify whether to stop the descent only after encountering two increasing scans, instead of stopping at the first increasing scan." />\n+ </when>\n+ <when value="none"/>\n+ </conditional>\n+ </inputs>\n+ <outputs>\n+ <data name="output_file" format="mzml" label="${on_string} centroided with refinement ${refinement.method}" from_work_dir="centroided.mzml"/>\n+ </outputs>\n+ <tests>\n+ <test>\n+ <param name="input_file" value="29_qc_no_dil_milliq_subset.mzML"/>\n+ <output name="output_file">\n+ <assert_contents>\n+ <expand macro="assertions_centroiding"/>\n+ </assert_contents>\n+ </output>\n+ </test>\n+ <test>\n+ <param name="input_file" value="29_qc_no_dil_milliq_subset.mzML"/>\n+ <param name="method" value="kNeighbors"/>\n+ <param name="k" value="3"/>\n+ <output name="output_file">\n+ <assert_contents>\n+ <expand macro="assertions_centroiding"/>\n+ </assert_contents>\n+ </output>\n+ </test>\n+ <test>\n+ <param name="input_file" value="29_qc_no_dil_milliq_subset.mzML"/>\n+ <param name="method" value="descendPeak"/>\n+ <param name="signal_percentage" value="10"/>\n+ <output name="output_file">\n+ <assert_contents>\n+ <expand macro="assertions_centroiding"/>\n+ </assert_contents>\n+ </output>\n+ </test>\n+ </tests>\n+ <help><![CDATA[\n+ .. class:: infomark\n+\n+**What it does**\n+\n+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.\n+\n+**Usage**\n+\n+- **Input**: Provide the input mzML file containing the mass spectrometry data to be centroided.\n+- **Parameters**:\n+ - **Input mzML File**: The input mzML file containing the mass spectrometry data to be centroided.\n+ - **MS2**: Specify if the dataset contains MS2 (tandem mass spectrometry) data.\n+ - **Half window size**: The number of data points on either side of the center point to include in the centroiding calculation.\n+ - **Noise estimation method**: Choose the method to estimate the noise in the spectrum. Options include Median Absolute Deviation (MAD) and Friedman\'s Super Smoother.\n+ - **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.\n+ - **Peak refinement method**: Select the method to refine the m/z value of the identified centroids. Options include None, K-Neighbors, and Descend Peak.\n+ - **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).\n+ - **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).\n+ - **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).\n+- **Output**: The centroided mzML file.\n+\n+**Input**\n+\n+- **Input mzML File**: The input mzML file containing the mass spectrometry data to be centroided.\n+\n+**Output**\n+\n+- **Output mzML File**: The resulting mzML file after applying the centroiding algorithm.\n+\n+**References**\n+\n+For more detailed information, please refer to the original documentation available via Bioconductor: https://bioconductor.org/packages/release/bioc/html/MSnbase.html\n+ ]]></help>\n+ <expand macro="citations"/>\n+</tool>\n\\ No newline at end of file\n' |
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| diff -r 000000000000 -r 4018639dc0a5 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Fri Jan 24 15:58:07 2025 +0000 |
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| @@ -0,0 +1,46 @@ +<macros> + <xml name="creator"> + <creator> + <person + givenName="Helge" + familyName="Hecht" + url="https://github.com/hechth" + identifier="0000-0001-6744-996X" /> + <organization + url="https://www.recetox.muni.cz/" + email="GalaxyToolsDevelopmentandDeployment@space.muni.cz" + name="RECETOX MUNI" /> + </creator> + </xml> + + <xml name="xrefs"> + <xrefs> + <xref type="bio.tools">msnbase</xref> + <xref type="bioconductor">msnbase</xref> + </xrefs> + </xml> + + <token name="@TOOL_VERSION@">2.32.0</token> + <token name="@VERSION_SUFFIX@">0</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">bioconductor-msnbase</requirement> + </requirements> + </xml> + <xml name="citations"> + <citations> + <citation type="doi">10.18129/B9.bioc.MSnbase</citation> + </citations> + </xml> + <xml name="assertions_smoothing"> + <has_text text='id="sf_ru_0"'/> + <has_text text="f3fdaed6b23f3690e004d16921be328018771bf1"/> + <has_n_lines n="1775"/> + </xml> + + <xml name="assertions_centroiding"> + <has_n_lines n="1512"/> + <has_text text='accession="MS:1000035" name="peak picking"'/> + <has_size size="129630" delta="50"/> + </xml> +</macros> \ No newline at end of file |
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| diff -r 000000000000 -r 4018639dc0a5 test-data/29_qc_no_dil_milliq_subset.mzML --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/29_qc_no_dil_milliq_subset.mzML Fri Jan 24 15:58:07 2025 +0000 |
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| b'@@ -0,0 +1,1844 @@\n+<?xml version="1.0" encoding="ISO-8859-1"?>\n+<indexedmzML xmlns="http://psi.hupo.org/ms/mzml" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psi.hupo.org/ms/mzml http://psidev.info/files/ms/mzML/xsd/mzML1.1.0_idx.xsd">\n+<mzML xmlns="http://psi.hupo.org/ms/mzml" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psi.hupo.org/ms/mzml http://psidev.info/files/ms/mzML/xsd/mzML1.1.0.xsd" accession="" version="1.1.0">\n+\t<cvList count="5">\n+\t\t<cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" URI="http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo"/>\n+\t\t<cv id="UO" fullName="Unit Ontology" URI="http://obo.cvs.sourceforge.net/obo/obo/ontology/phenotype/unit.obo"/>\n+\t\t<cv id="BTO" fullName="BrendaTissue545" version="unknown" 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