comparison abims_xcms_xcmsSet.xml @ 37:9ada611dd63f draft

planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 3922356e5edae763800a4311146e2fdeb52c296e

36:d39b9aff9cf7

            mzIntervalExtension $sectionROI.mzIntervalExtension
            polarity $sectionROI.polarity
        #elif $methods.method == "MatchedFilter":
            fwhm $methods.fwhm
            binSize $methods.binSize
            impute $methods.impute_cond.impute
            #if $methods.impute_cond.impute == "linbase":
                #if $methods.impute_cond.baseValue != "":
                    baseValue $methods.impute_cond.baseValue
                #end if
                distance $methods.impute_cond.distance
            #end if
            ## Advanced
            #if $methods.MatchedFilterAdv.sigma != "":
                sigma $methods.MatchedFilterAdv.sigma
            #end if
            max $methods.MatchedFilterAdv.max
            snthresh $methods.MatchedFilterAdv.snthresh

            <!-- MatchedFilter -->
            <when value="MatchedFilter">
                <param argument="fwhm" type="integer" value="30" label="Full width at half maximum of matched filtration gaussian model peak" help="Only used to calculate the actual sigma" />
                <param argument="binSize" type="float" value="0.1" label="Step size to use for profile generation" help="The peak detection algorithm creates extracted ion base peak chromatograms (EIBPC) on a fixed step size. (Previously step)" />
                <conditional name="impute_cond">
                    <param argument="impute" type="select" label="Method to be used for missing value imputation" help="(previously profmethod)">
                        <option value="none">none - no linear interpolation</option>
                        <option value="lin">lin - linear interpolation</option>
                        <option value="linbase">linbase - linear interpolation within a certain bin-neighborhood</option>
                        <option value="intlin">intlin - integral of the linearly interpolated data from plus to minus half the step size</option>
                    </param>
                    <when value="none" />
                    <when value="lin" />
                    <when value="linbase">
                        <param argument="baseValue" type="float" value="" optional="true" label="The base value to which empty elements should be set" help="The default for the ‘baseValue’ is half of the smallest value in ‘x’ (‘NA’s being removed)." />
                        <param argument="distance" type="integer" value="0" label="Number of non-empty neighboring element of an empty element that should be considered for linear interpolation." />
                    </when>
                    <when value="intlin" />
                </conditional>
                <section name="MatchedFilterAdv" title="Advanced Options" expanded="False">
                    <param argument="sigma" type="float" value="" optional="true" label="Standard deviation (width) of matched filtration model peak" help="Leave it to empty to calculate it using fwhm by default at fwhm/2.3548" />
                    <param argument="max" type="integer" value="5" label="Maximum number of peaks that are expected/will be identified per slice" />
                    <param argument="snthresh" type="integer" value="10" label="Signal to Noise ratio cutoff" help="defining the signal to noise cutoff to be used in the chromatographic peak detection step" />
                    <param argument="steps" type="integer" value="2" label="Number of bins to be merged before filtration" help="(i.e. the number of neighboring bins that will be joined to the slice in which filtration and peak detection will be performed)" />
                    <param argument="mzdiff" type="float" value="0.6" label="Minimum difference in m/z for peaks with overlapping Retention Times" help="By default: 0.8-step*steps " />

                <has_text text="Peak Groups: 0" />
                <has_text text="Sample classes: KO, WT" />
            </assert_stdout>
        </test>-->
        <test>
            <param name="image" value="ko15-raw.Rdata" ftype="rdata" />
            <conditional name="methods">
                <param name="method" value="CentWave" />
                <param name="ppm" value="25" />
                <param name="peakwidth" value="20,50" />
            </conditional>

                <has_text text="Peak Groups: 0" />
                <has_text text="Sample classes: ." />
            </assert_stdout>
        </test>
        <!-- DISABLE FOR TRAVIS
        Useful to generate test-data for the further steps -->
        <test>
            <param name="image" value="ko16-raw.Rdata" ftype="rdata" />
            <conditional name="methods">
                <param name="method" value="CentWave" />
                <param name="ppm" value="25" />
                <param name="peakwidth" value="20,50" />
            </conditional>

                <has_text text="Peak Groups: 0" />
                <has_text text="Sample classes: ." />
            </assert_stdout>
        </test>
        <test>
            <param name="image" value="wt15-raw.Rdata" ftype="rdata" />
            <conditional name="methods">
                <param name="method" value="CentWave" />
                <param name="ppm" value="25" />
                <param name="peakwidth" value="20,50" />
            </conditional>

                <has_text text="Peak Groups: 0" />
                <has_text text="Sample classes: ." />
            </assert_stdout>
        </test>
        <test>
            <param name="image" value="wt16-raw.Rdata" ftype="rdata" />
            <conditional name="methods">
                <param name="method" value="CentWave" />
                <param name="ppm" value="25" />
                <param name="peakwidth" value="20,50" />
            </conditional>

                <has_text text="Peaks: 2303 (about 2303 per sample)" />
                <has_text text="Peak Groups: 0" />
                <has_text text="Sample classes: ." />
            </assert_stdout>
        </test>
        
        <!-- DISABLE FOR TRAVIS
        Test to test the different methods parameters
        <test>
            <param name="image" value="ko15-raw.Rdata" ftype="rdata" />
            <conditional name="methods">
                <param name="method" value="MatchedFilter" />
                <param name="fwhm" value="35" />
                <conditional name="impute_cond">
                    <param name="impute" value="linbase" />
                    <param name="baseValue" value="0.1" />
                    <param name="distance" value="1" />
                </conditional>
            </conditional>
            <assert_stdout>
                <has_text text="fwhm: 35" />
                <has_text text="impute: linbase" />
                <has_text text="baseValue: 0.1" />
                <has_text text="distance: 1" />
            </assert_stdout>
        </test>
        <test>
            <param name="image" value="ko15-raw.Rdata" ftype="rdata" />
            <conditional name="methods">
                <param name="method" value="CentWavePredIso" />
                <param name="ppm" value="56" />
                <param name="peakwidth" value="5.275,13.5" />
                <section name="CentWaveAdvROI">

                <has_text text="  scmin scmax mzmin mzmax length intensity" />
                <has_text text="1   200   300   300   350    100      5000" />
            </assert_stdout>
        </test>
        <test>
            <param name="image" value="ko15-raw.Rdata" ftype="rdata" />
            <conditional name="methods">
                <param name="method" value="MSW" />
                <param name="snthresh" value="4" />
                <param name="verboseColumns" value="true" />
            </conditional>

    | Tabular file that contains for each sample, it's associated class and polarity (positive,negative and mixed).
    | This file is necessary in the Anova and PCA step of the workflow.

xset.RData: rdata.xcms.findchrompeaks format

    | Rdata file that is necessary in the second step of the workflow "xcms.group".

---------------------------------------------------

Changelog/News
--------------

37:9ada611dd63f

            mzIntervalExtension $sectionROI.mzIntervalExtension
            polarity $sectionROI.polarity
        #elif $methods.method == "MatchedFilter":
            fwhm $methods.fwhm
            binSize $methods.binSize
            ## Advanced
            impute $methods.MatchedFilterAdv.impute_cond.impute
            #if $methods.MatchedFilterAdv.impute_cond.impute == "linbase":
                #if $methods.MatchedFilterAdv.impute_cond.baseValue != "":
                    baseValue $methods.MatchedFilterAdv.impute_cond.baseValue
                #end if
                distance $methods.MatchedFilterAdv.impute_cond.distance
            #end if
            #if $methods.MatchedFilterAdv.sigma != "":
                sigma $methods.MatchedFilterAdv.sigma
            #end if
            max $methods.MatchedFilterAdv.max
            snthresh $methods.MatchedFilterAdv.snthresh

            <!-- MatchedFilter -->
            <when value="MatchedFilter">
                <param argument="fwhm" type="integer" value="30" label="Full width at half maximum of matched filtration gaussian model peak" help="Only used to calculate the actual sigma" />
                <param argument="binSize" type="float" value="0.1" label="Step size to use for profile generation" help="The peak detection algorithm creates extracted ion base peak chromatograms (EIBPC) on a fixed step size. (Previously step)" />
                <section name="MatchedFilterAdv" title="Advanced Options" expanded="False">
                    <conditional name="impute_cond">
                        <param argument="impute" type="select" label="Method to be used for missing value imputation" help="(previously profmethod)">
                            <option value="none">none - no linear interpolation</option>
                            <option value="lin">lin - linear interpolation</option>
                            <option value="linbase">linbase - linear interpolation within a certain bin-neighborhood</option>
                            <option value="intlin">intlin - integral of the linearly interpolated data from plus to minus half the step size</option>
                        </param>
                        <when value="none" />
                        <when value="lin" />
                        <when value="linbase">
                            <param argument="baseValue" type="float" value="" optional="true" label="The base value to which empty elements should be set" help="The default for the ‘baseValue’ is half of the smallest value in ‘x’ (‘NA’s being removed)." />
                            <param argument="distance" type="integer" value="0" label="Number of non-empty neighboring element of an empty element that should be considered for linear interpolation." />
                        </when>
                        <when value="intlin" />
                    </conditional>
                    <param argument="sigma" type="float" value="" optional="true" label="Standard deviation (width) of matched filtration model peak" help="Leave it to empty to calculate it using fwhm by default at fwhm/2.3548" />
                    <param argument="max" type="integer" value="5" label="Maximum number of peaks that are expected/will be identified per slice" />
                    <param argument="snthresh" type="integer" value="10" label="Signal to Noise ratio cutoff" help="defining the signal to noise cutoff to be used in the chromatographic peak detection step" />
                    <param argument="steps" type="integer" value="2" label="Number of bins to be merged before filtration" help="(i.e. the number of neighboring bins that will be joined to the slice in which filtration and peak detection will be performed)" />
                    <param argument="mzdiff" type="float" value="0.6" label="Minimum difference in m/z for peaks with overlapping Retention Times" help="By default: 0.8-step*steps " />

                <has_text text="Peak Groups: 0" />
                <has_text text="Sample classes: KO, WT" />
            </assert_stdout>
        </test>-->
        <test>
            <param name="image" value="ko15-raw.RData" ftype="rdata" />
            <conditional name="methods">
                <param name="method" value="CentWave" />
                <param name="ppm" value="25" />
                <param name="peakwidth" value="20,50" />
            </conditional>

                <has_text text="Peak Groups: 0" />
                <has_text text="Sample classes: ." />
            </assert_stdout>
        </test>
        <!-- DISABLE FOR TRAVIS
        Useful to generate test-data for the further steps
        <test>
            <param name="image" value="ko16-raw.RData" ftype="rdata" />
            <conditional name="methods">
                <param name="method" value="CentWave" />
                <param name="ppm" value="25" />
                <param name="peakwidth" value="20,50" />
            </conditional>

                <has_text text="Peak Groups: 0" />
                <has_text text="Sample classes: ." />
            </assert_stdout>
        </test>
        <test>
            <param name="image" value="wt15-raw.RData" ftype="rdata" />
            <conditional name="methods">
                <param name="method" value="CentWave" />
                <param name="ppm" value="25" />
                <param name="peakwidth" value="20,50" />
            </conditional>

                <has_text text="Peak Groups: 0" />
                <has_text text="Sample classes: ." />
            </assert_stdout>
        </test>
        <test>
            <param name="image" value="wt16-raw.RData" ftype="rdata" />
            <conditional name="methods">
                <param name="method" value="CentWave" />
                <param name="ppm" value="25" />
                <param name="peakwidth" value="20,50" />
            </conditional>

                <has_text text="Peaks: 2303 (about 2303 per sample)" />
                <has_text text="Peak Groups: 0" />
                <has_text text="Sample classes: ." />
            </assert_stdout>
        </test>
        -->
        <!-- DISABLE FOR TRAVIS
        Test to test the different methods parameters
        <test>
            <param name="image" value="ko15-raw.RData" ftype="rdata" />
            <conditional name="methods">
                <param name="method" value="MatchedFilter" />
                <param name="fwhm" value="35" />
                <section name="MatchedFilterAdv"
                    <conditional name="impute_cond">
                        <param name="impute" value="linbase" />
                        <param name="baseValue" value="0.1" />
                        <param name="distance" value="1" />
                    </conditional>
                </section>
            </conditional>
            <assert_stdout>
                <has_text text="fwhm: 35" />
                <has_text text="impute: linbase" />
                <has_text text="baseValue: 0.1" />
                <has_text text="distance: 1" />
            </assert_stdout>
        </test>
        <test>
            <param name="image" value="ko15-raw.RData" ftype="rdata" />
            <conditional name="methods">
                <param name="method" value="CentWavePredIso" />
                <param name="ppm" value="56" />
                <param name="peakwidth" value="5.275,13.5" />
                <section name="CentWaveAdvROI">

                <has_text text="  scmin scmax mzmin mzmax length intensity" />
                <has_text text="1   200   300   300   350    100      5000" />
            </assert_stdout>
        </test>
        <test>
            <param name="image" value="ko15-raw.RData" ftype="rdata" />
            <conditional name="methods">
                <param name="method" value="MSW" />
                <param name="snthresh" value="4" />
                <param name="verboseColumns" value="true" />
            </conditional>

    | Tabular file that contains for each sample, it's associated class and polarity (positive,negative and mixed).
    | This file is necessary in the Anova and PCA step of the workflow.

xset.RData: rdata.xcms.findchrompeaks format

    | RData file that is necessary in the second step of the workflow "xcms.group".

---------------------------------------------------

Changelog/News
--------------