diff bioconductor_msnbase_centroid.xml @ 0:4018639dc0a5 draft default tip

planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-msnbase commit 8a94b9932a94c323a33dfe858ee0a2c57fb04701

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+++ b/bioconductor_msnbase_centroid.xml	Fri Jan 24 15:58:07 2025 +0000
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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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