comparison abims_xcms_xcmsSet.xml @ 33:c363b9f1caef draft

planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 7b226c3ba91a3cf654ec1c14b3ef85090968bb0f

32:2bf1cb023c94

        #else
            zipfile '$input'
        #end if

        BPPARAM \${GALAXY_SLOTS:-1}
        method $methods.method

        #if $methods.method == "CentWave":
            ppm $methods.ppm
            peakwidth "c($methods.peakwidth)"

    <inputs>

        <param name="input" type="data" format="mzxml,mzml,mzdata,netcdf,no_unzip.zip,zip" label="File(s) from your history containing your chromatograms" help="Single file mode for the format: mzxml, mzml, mzdata and netcdf. Zip file mode for the format: no_unzip.zip, zip. See the help section below." />

        <!--@TODO <param argument="scanrange" type="text" value="" label="scanrange" help="scan range to process, for example (16,365)" >
        Should be replaced by MSnBase::filterAcquisition
        -->

        <conditional name="methods">
            <param name="method" type="select" label="Extraction method for peaks detection" help="[method] See the help section below">
                <option value="MatchedFilter" selected="true">MatchedFilter - peak detection in chromatographic space</option>
                <option value="CentWave">CentWave - chromatographic peak detection using the centWave method</option>
                <option value="MSW">MSW - single-spectrum non-chromatography MS data peak detection</option>
            </param>

            <!-- centWave Filter options -->
            <when value="CentWave">
                <param argument="ppm" type="integer" value="25" label="Max tolerated ppm m/z deviation in consecutive scans in ppm" help="for the initial ROI definition." />
                <param argument="peakwidth" type="text" value="20,50" label="Min,Max peak width in seconds" help="with the expected approximate peak width in chromatographic space." />

                <section name="CentWaveAdv" title="Advanced Options" expanded="False">
                    <param argument="snthresh" type="integer" value="10" label="Signal to Noise ratio cutoff" />
                    <param argument="prefilter" type="text" value="3,100" label="Prefilter step for for the first analysis step (ROI detection)" help="Separate by coma k, I. Mass traces are only retained if they contain at least ‘k‘ peaks with intensity ‘>= I‘." />
                    <param argument="mzCenterFun" type="select" label="Name of the function to calculate the m/z center of the chromatographic peak" >
                        <option value="wMean">intensity weighted mean of the peak's m/z values</option>
                        <option value="mean">mean of the peak's m/z values</option>
                        <option value="apex">use the m/z value at the peak apex</option>
                        <option value="wMeanApex3">ntensity weighted mean of the m/z value at the peak apex and the m/z values left and right of it</option>

            <!-- MSW Filter options -->
            <when value="MSW">
                <!---@TODO <param argument="winSize_noise" type="integer" value="500" label="The local window size to estimate the noise level" help="[winSize.noise]" />-->
                <param argument="snthresh" type="integer" value="3" label="Signal to Noise ratio cutoff" help="" />
                <param argument="verboseColumns" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="verbose Columns" help="whether additional peak meta data columns should be returned" />
                <param argument="scales" type="text" value="1,2,4,6,8,10,12,14,16,18,20,22,24,26,28,30,32,36,40,44,48,52,56,60,64" label="Scales of the Continuous Wavelet Transform (CWT)" help="Scales are linked to the width of the peaks that are to be detected." />
                <param argument="nearbyPeak" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Determine whether to include the nearby small peaks of major peaks" />
                <!-- peakScaleRange -->
                <param argument="ampTh" type="float" value="0.01" label="Minimum required relative amplitude of the peak" help="Ratio to the maximum of CWT coefficients" />
                <!-- minNoiseLevel -->
                <!-- ridgeLength -->

    <tests>

        <test>
            <param name="input" value="faahKO_reduce.zip"  ftype="zip" />
            <conditional name="methods">
                <param name="method" value="CentWave" />
                <param name="ppm" value="25" />
                <param name="peakwidth" value="20,50" />
            </conditional>
            <assert_stdout>
                <has_text text="ppm: 25" />
                <has_text text="peakwidth: 20, 50" />
                <has_text text="object with 4 samples" />
                <has_text text="Time range: 2506.1-4477.9 seconds (41.8-74.6 minutes)" />
                <has_text text="Mass range: 200.1-600 m/z" />
                <has_text text="Peaks: 9251 (about 2313 per sample)" />
                <has_text text="Peak Groups: 0" />
                <has_text text="Sample classes: KO, WT" />
            </assert_stdout>
        </test>
        <test>

**Version 3.0.0.0 - 14/02/2018**

- UPGRADE: upgrade the xcms version from 1.46.0 to 3.0.0. So refactoring of a lot of underlining codes and methods

- NEW: a bunch of new options: CentWave.mzCenterFun, CentWave.fitgauss, CentWave.verboseColumns, MatchedFilter.sigma

- UPDATE: since xcms 3.0.0, some options are no more available: scanrange, profmethod, MatchedFilter.step, MatchedFilter.sigma, MSW.winSize.noise, MSW.SNR.method

**Version 2.1.1 - 29/11/2017**

33:c363b9f1caef

        #else
            zipfile '$input'
        #end if

        BPPARAM \${GALAXY_SLOTS:-1}

        #if $filterSection.filterAcquisitionNum != "":
            filterAcquisitionNum "c($filterSection.filterAcquisitionNum)"
        #end if
        #if $filterSection.filterRt != "":
            filterRt "c($filterSection.filterRt)"
        #end if
        #if $filterSection.filterMz != "":
            filterMz "c($filterSection.filterMz)"
        #end if

        method $methods.method

        #if $methods.method == "CentWave":
            ppm $methods.ppm
            peakwidth "c($methods.peakwidth)"

    <inputs>

        <param name="input" type="data" format="mzxml,mzml,mzdata,netcdf,no_unzip.zip,zip" label="File(s) from your history containing your chromatograms" help="Single file mode for the format: mzxml, mzml, mzdata and netcdf. Zip file mode for the format: no_unzip.zip, zip. See the help section below." />

        <section name="filterSection" title="Spectra Filters" expanded="False">
            <param argument="filterAcquisitionNum" type="text" value="" optional="true" label="Filter on Acquisition Numbers" help="min,max">
                <expand macro="input_validator_range_integer"/>
            </param>
            <param argument="filterRt" type="text" value="" optional="true" label="Filter on Retention Time" help="min,max">
                <expand macro="input_validator_range_integer"/>
            </param>
            <param argument="filterMz" type="text" value="" optional="true" label="Filter on Mz" help="min,max">
                <expand macro="input_validator_range_integer"/>
            </param>
        </section>

        <conditional name="methods">
            <param name="method" type="select" label="Extraction method for peaks detection" help="See the help section below">
                <option value="MatchedFilter" selected="true">MatchedFilter - peak detection in chromatographic space</option>
                <option value="CentWave">CentWave - chromatographic peak detection using the centWave method</option>
                <option value="MSW">MSW - single-spectrum non-chromatography MS data peak detection</option>
            </param>

            <!-- centWave Filter options -->
            <when value="CentWave">
                <param argument="ppm" type="integer" value="25" label="Max tolerated ppm m/z deviation in consecutive scans in ppm" help="for the initial ROI definition." />
                <param argument="peakwidth" type="text" value="20,50" label="Min,Max peak width in seconds" help="with the expected approximate peak width in chromatographic space.">
                    <expand macro="input_validator_range_float"/>
                </param>

                <section name="CentWaveAdv" title="Advanced Options" expanded="False">
                    <param argument="snthresh" type="integer" value="10" label="Signal to Noise ratio cutoff" />
                    <param argument="prefilter" type="text" value="3,100" label="Prefilter step for for the first analysis step (ROI detection)" help="Separate by coma k, I. Mass traces are only retained if they contain at least ‘k‘ peaks with intensity ‘>= I‘.">
                        <expand macro="input_validator_range_integer"/>
                    </param>
                    <param argument="mzCenterFun" type="select" label="Name of the function to calculate the m/z center of the chromatographic peak" >
                        <option value="wMean">intensity weighted mean of the peak's m/z values</option>
                        <option value="mean">mean of the peak's m/z values</option>
                        <option value="apex">use the m/z value at the peak apex</option>
                        <option value="wMeanApex3">ntensity weighted mean of the m/z value at the peak apex and the m/z values left and right of it</option>

            <!-- MSW Filter options -->
            <when value="MSW">
                <!---@TODO <param argument="winSize_noise" type="integer" value="500" label="The local window size to estimate the noise level" help="[winSize.noise]" />-->
                <param argument="snthresh" type="integer" value="3" label="Signal to Noise ratio cutoff" help="" />
                <param argument="verboseColumns" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="verbose Columns" help="whether additional peak meta data columns should be returned" />
                <param argument="scales" type="text" value="1,2,4,6,8,10,12,14,16,18,20,22,24,26,28,30,32,36,40,44,48,52,56,60,64" label="Scales of the Continuous Wavelet Transform (CWT)" help="Scales are linked to the width of the peaks that are to be detected." >
                    <expand macro="input_validator_list_integer"/>
                </param>
                <param argument="nearbyPeak" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Determine whether to include the nearby small peaks of major peaks" />
                <!-- peakScaleRange -->
                <param argument="ampTh" type="float" value="0.01" label="Minimum required relative amplitude of the peak" help="Ratio to the maximum of CWT coefficients" />
                <!-- minNoiseLevel -->
                <!-- ridgeLength -->

    <tests>

        <test>
            <param name="input" value="faahKO_reduce.zip"  ftype="zip" />
            <section name="filterSection">
                <param name="filterAcquisitionNum" value="100,5000" />
                <param name="filterRt" value="3000,4000" />
                <param name="filterMz" value="300,400" />
            </section>
            <conditional name="methods">
                <param name="method" value="CentWave" />
                <param name="ppm" value="25" />
                <param name="peakwidth" value="20,50" />
            </conditional>
            <assert_stdout>
                <has_text text="ppm: 25" />
                <has_text text="peakwidth: 20, 50" />
                <has_text text="object with 4 samples" />
                <has_text text="Time range: 3006.9-3978.7 seconds (50.1-66.3 minutes)" />
                <has_text text="Mass range: 300-400 m/z" />
                <has_text text="Peaks: 1311 (about 328 per sample)" />
                <has_text text="Peak Groups: 0" />
                <has_text text="Sample classes: KO, WT" />
            </assert_stdout>
        </test>
        <test>

**Version 3.0.0.0 - 14/02/2018**

- UPGRADE: upgrade the xcms version from 1.46.0 to 3.0.0. So refactoring of a lot of underlining codes and methods

- NEW: a bunch of new options: Spectra Filters, CentWave.mzCenterFun, CentWave.fitgauss, CentWave.verboseColumns, MatchedFilter.sigma

- UPDATE: since xcms 3.0.0, some options are no more available: scanrange, profmethod, MatchedFilter.step, MatchedFilter.sigma, MSW.winSize.noise, MSW.SNR.method

**Version 2.1.1 - 29/11/2017**