diff --git a/tools/bioconductor-msnbase/.shed.yml b/tools/bioconductor-msnbase/.shed.yml
new file mode 100644
index 000000000..d6a0b1e6a
--- /dev/null
+++ b/tools/bioconductor-msnbase/.shed.yml
@@ -0,0 +1,21 @@
+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
diff --git a/tools/bioconductor-msnbase/bioconductor_msnbase_centroid.xml b/tools/bioconductor-msnbase/bioconductor_msnbase_centroid.xml
new file mode 100644
index 000000000..4c8f5ac00
--- /dev/null
+++ b/tools/bioconductor-msnbase/bioconductor_msnbase_centroid.xml
@@ -0,0 +1,142 @@
+<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>
\ No newline at end of file
diff --git a/tools/bioconductor-msnbase/bioconductor_msnbase_smooth_chromatogram.xml b/tools/bioconductor-msnbase/bioconductor_msnbase_smooth_chromatogram.xml
new file mode 100644
index 000000000..1f637280b
--- /dev/null
+++ b/tools/bioconductor-msnbase/bioconductor_msnbase_smooth_chromatogram.xml
@@ -0,0 +1,105 @@
+<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>
\ No newline at end of file
diff --git a/tools/bioconductor-msnbase/bioconductor_msnbase_smooth_mz.xml b/tools/bioconductor-msnbase/bioconductor_msnbase_smooth_mz.xml
new file mode 100644
index 000000000..11e243447
--- /dev/null
+++ b/tools/bioconductor-msnbase/bioconductor_msnbase_smooth_mz.xml
@@ -0,0 +1,105 @@
+<tool id="bioconductor_msnbase_smooth_mz" name="bioconductor-msnbase smooth mz" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0" license="MIT">
+    <description>smooth raw MS data in mass-to-charge ratio domain</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")
+            #if $smoothing.method == "SavitzkyGolay"
+            data_smoothed <- MSnbase::smooth(data_prof, method = "$method", halfWindowSize = $halfWindowSize, polynomialOrder = $smoothing.polynomial)
+            #else if $smoothing.method == "MovingAverage"
+            data_smoothed <- MSnbase::smooth(data_prof, method = "$method", halfWindowSize = $halfWindowSize, weighted = $smoothing.weighted)
+            #end if
+            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 raw MS data."/>
+        <conditional name="smoothing">
+            <param name="method" type="select" label="Smoothing Method" help="The smoothing method to use.">
+                <option value="SavitzkyGolay" selected="true">Savitzky-Golay</option>
+                <option value="MovingAverage">Moving Average</option>
+            </param>
+            <when value="SavitzkyGolay">
+                <param label="polynomialOrder" name="polynomial" value="3" min="1" max="7" type="integer" 
+                    help="Polynomial order for the Savitzky-Golay filter. This determines the degree of the polynomial used for smoothing."/>
+            </when>
+            <when value="MovingAverage">
+                <param argument="weighted" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Weighted" 
+                    help="Whether to weight the moving average depending on the distance from the centre. If checked, the moving average will be weighted."/>
+            </when>
+        </conditional>
+        <param name="halfWindowSize" type="integer" label="Half window size" min="2" value="4" 
+            help="The half window size parameter for the smoothing method. This determines the number of points on either side of the central point to include in the smoothing window."/>
+    </inputs>
+    <outputs>
+        <data name="output_file" format="mzml" label="Smoothed ${on_string} using ${method}" 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="319526" delta="100"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="input_file" value="29_qc_no_dil_milliq_subset.mzML"/>
+            <param name="method" value="MovingAverage"/>
+            <param name="weighted" value="TRUE"/>
+            <output name="output_file">
+                <assert_contents>
+                    <expand macro="assertions_smoothing"/>
+                    <has_size size="308803" delta="100"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+.. class:: infomark
+
+**What it does**
+
+This tool performs smoothing of MSnbase data using Bioconductor. It supports Savitzky-Golay and Moving Average smoothing methods. Smoothing is a technique used to reduce noise and improve the signal quality in mass spectrometry data.
+
+- **Parameters**
+    - **Input mzML File**: The input mzML file containing the data to be smoothed. This file should be in mzML format.
+    - **Smoothing Method**: The smoothing method to use. Options are:
+        - **Savitzky-Golay**: A digital filter that can smooth data while preserving the shape and height of waveform peaks.
+            - **Polynomial Order**: The polynomial order for the Savitzky-Golay filter. This determines the degree of the polynomial used for smoothing. The default value is 3, and it can range from 1 to 7.
+        - **Moving Average**: A simple and commonly used method for smoothing data by averaging adjacent points.
+            - **Weighted**: Whether to weight the moving average depending on the distance from the centre. If checked, the moving average will be weighted.
+    - **Half Window Size**: The half window size parameter for the smoothing method. This determines the number of points on either side of the central point to include in the smoothing window. The default value is 4, and it must be at least 2.
+
+**Output**
+
+- **Smoothed mzML File**: The output mzML file with smoothed data. The file will be in mzML format.
+     ]]></help>
+        <expand macro="citations"/>
+</tool>
\ No newline at end of file
diff --git a/tools/bioconductor-msnbase/macros.xml b/tools/bioconductor-msnbase/macros.xml
new file mode 100644
index 000000000..f0971e3fd
--- /dev/null
+++ b/tools/bioconductor-msnbase/macros.xml
@@ -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
diff --git a/tools/bioconductor-msnbase/test-data/29_qc_no_dil_milliq_subset.mzML b/tools/bioconductor-msnbase/test-data/29_qc_no_dil_milliq_subset.mzML
new file mode 100644
index 000000000..7acd2b77f
--- /dev/null
+++ b/tools/bioconductor-msnbase/test-data/29_qc_no_dil_milliq_subset.mzML
@@ -0,0 +1,1844 @@
+<?xml version="1.0" encoding="ISO-8859-1"?>
+<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">
+<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">
+	<cvList count="5">
+		<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"/>
+		<cv id="UO" fullName="Unit Ontology" URI="http://obo.cvs.sourceforge.net/obo/obo/ontology/phenotype/unit.obo"/>
+		<cv id="BTO" fullName="BrendaTissue545" version="unknown" URI="http://www.brenda-enzymes.info/ontology/tissue/tree/update/update_files/BrendaTissueOBO"/>
+		<cv id="GO" fullName="Gene Ontology - Slim Versions" version="unknown" URI="http://www.geneontology.org/GO_slims/goslim_goa.obo"/>
+		<cv id="PATO" fullName="Quality ontology" version="unknown" URI="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/quality.obo"/>
+	</cvList>
+	<fileDescription>
+		<fileContent>
+			<cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" />
+		</fileContent>
+		<sourceFileList count="1">
+			<sourceFile id="sf_ru_0" name="Galaxy1-[29_qc_no_dil_milliq.mzml].mzml" location="file:///C:/Users/473355/Downloads">
+				<cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="f3fdaed6b23f3690e004d16921be328018771bf1" />
+				<cvParam cvRef="MS" accession="MS:1000584" name="mzML format" />
+				<cvParam cvRef="MS" accession="MS:1000768" name="Thermo nativeID format" />
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