view bioconductor_msnbase_smooth_chromatogram.xml @ 0:492350f45be9 draft default tip

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

<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>