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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-msnbase commit 8a94b9932a94c323a33dfe858ee0a2c57fb04701
author recetox
date Fri, 24 Jan 2025 15:58:07 +0000
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1 <tool id="bioconductor_msnbase_centroid" name="bioconductor-msnbase centroid" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01" license="MIT">
2 <description>centroid raw profile-mode MS data</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="xrefs"/>
7 <expand macro="creator"/>
8 <expand macro="requirements"/>
9 <command detect_errors="exit_code"><![CDATA[
10 Rscript "${run_script}"
11 ]]></command>
12 <configfiles>
13 <configfile name="run_script"><![CDATA[
14 data_prof <- MSnbase::readMSData("$input_file", msLevel = $mslevel)
15
16 data_centroided <- MSnbase::pickPeaks(
17 data_prof,
18 halfWindowSize = ${halfWindowSize},
19 method = "${estimate_noise_method}",
20 SNR = ${snr},
21 refineMz = "${refinement.method}",
22 #if "$refinement.method" == "kNeighbors"
23 k = ${refinement.k}
24 #else if "$refinement.method" == "descendPeak"
25 signalPercentage = ${refinement.signal_percentage},
26 stopAtTwo = ${refinement.stop_at_two}
27 #end if
28 )
29
30 MSnbase::writeMSData(
31 data_centroided,
32 file = "centroided.mzml",
33 copy = TRUE,
34 outformat = "mzml"
35 )
36 ]]></configfile>
37 </configfiles>
38 <inputs>
39 <param name="input_file" type="data" format="mzml" label="Input mzML File"
40 help="The input mzML file containing the mass spectrometry data to be centroided."/>
41 <param argument="mslevel" type="boolean" truevalue="2" falsevalue="1" checked="false" label="MS2"
42 help="Specify if the dataset contains MS2 (tandem mass spectrometry) data." />
43 <param name="halfWindowSize" type="integer" label="Half window size" min="1" value="2"
44 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."/>
45 <param name="estimate_noise_method" type="select" label="Noise estimation method"
46 help="Method to choose to estimate the noise in the spectrum.">
47 <option value="MAD" selected="true">Median Absolute Deviation</option>
48 <option value="SuperSmoother">Friedman's Super Smoother</option>
49 </param>
50 <param argument="--snr" type="float" min="0" value="3" label="Signal-to-noise ratio (SNR)"
51 help="The signal-to-noise ratio threshold for removing noisy signals." />
52 <conditional name="refinement">
53 <param name="method" type="select" label="Peak refinement method"
54 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.
55 The m/z value is calculated as an intensity weighted average of the m/z values within the peak region.
56 How the peak region is defined depends on the method chosen.">
57 <option value="none" selected="true">None</option>
58 <option value="kNeighbors">K-Neighbors</option>
59 <option value="descendPeak">Descend Peak</option>
60 </param>
61 <when value="kNeighbors">
62 <param argument="--k" type="integer" min="1" max="10" value="2" label="K"
63 help="The number of 2*K nearest neighbors to consider for m/z interpolation during peak refinement."/>
64 </when>
65 <when value="descendPeak">
66 <param argument="--signal_percentage" type="integer" min="0" max="100" value="20" label="Intensity threshold (%)"
67 help="The signal intensity cutoff threshold (as a percentage) for including values in the m/z calculation during peak refinement." />
68 <param argument="stop_at_two" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Stop at two"
69 help="Specify whether to stop the descent only after encountering two increasing scans, instead of stopping at the first increasing scan." />
70 </when>
71 <when value="none"/>
72 </conditional>
73 </inputs>
74 <outputs>
75 <data name="output_file" format="mzml" label="${on_string} centroided with refinement ${refinement.method}" from_work_dir="centroided.mzml"/>
76 </outputs>
77 <tests>
78 <test>
79 <param name="input_file" value="29_qc_no_dil_milliq_subset.mzML"/>
80 <output name="output_file">
81 <assert_contents>
82 <expand macro="assertions_centroiding"/>
83 </assert_contents>
84 </output>
85 </test>
86 <test>
87 <param name="input_file" value="29_qc_no_dil_milliq_subset.mzML"/>
88 <param name="method" value="kNeighbors"/>
89 <param name="k" value="3"/>
90 <output name="output_file">
91 <assert_contents>
92 <expand macro="assertions_centroiding"/>
93 </assert_contents>
94 </output>
95 </test>
96 <test>
97 <param name="input_file" value="29_qc_no_dil_milliq_subset.mzML"/>
98 <param name="method" value="descendPeak"/>
99 <param name="signal_percentage" value="10"/>
100 <output name="output_file">
101 <assert_contents>
102 <expand macro="assertions_centroiding"/>
103 </assert_contents>
104 </output>
105 </test>
106 </tests>
107 <help><![CDATA[
108 .. class:: infomark
109
110 **What it does**
111
112 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.
113
114 **Usage**
115
116 - **Input**: Provide the input mzML file containing the mass spectrometry data to be centroided.
117 - **Parameters**:
118 - **Input mzML File**: The input mzML file containing the mass spectrometry data to be centroided.
119 - **MS2**: Specify if the dataset contains MS2 (tandem mass spectrometry) data.
120 - **Half window size**: The number of data points on either side of the center point to include in the centroiding calculation.
121 - **Noise estimation method**: Choose the method to estimate the noise in the spectrum. Options include Median Absolute Deviation (MAD) and Friedman's Super Smoother.
122 - **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.
123 - **Peak refinement method**: Select the method to refine the m/z value of the identified centroids. Options include None, K-Neighbors, and Descend Peak.
124 - **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).
125 - **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).
126 - **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).
127 - **Output**: The centroided mzML file.
128
129 **Input**
130
131 - **Input mzML File**: The input mzML file containing the mass spectrometry data to be centroided.
132
133 **Output**
134
135 - **Output mzML File**: The resulting mzML file after applying the centroiding algorithm.
136
137 **References**
138
139 For more detailed information, please refer to the original documentation available via Bioconductor: https://bioconductor.org/packages/release/bioc/html/MSnbase.html
140 ]]></help>
141 <expand macro="citations"/>
142 </tool>