comparison abims_xcms_xcmsSet.xml @ 39:e8d7395a70b2 draft

planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e131bacd37bfaf2c4132fd214c81db9b8a9df513

38:e66eeca443e4

                    </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 " />
                    <!-- index -->
                </section>
            </when>

            <!-- CentWaveWithPredIsoROIs -->

-----------
Description
-----------

This tool is used for preprocessing data from multiple LC/MS files (formats NetCDF, mzXML and mzData) using the xcms_ R package. It extracts ion from each sample independently and using a statistic model, peaks are filtered and integrated.
You can read a tutorial on how to perform xcms preprocessing which is available here_.

.. _xcms: https://bioconductor.org/packages/release/bioc/html/xcms.html
.. _here: http://web11.sb-roscoff.fr/download/w4m/howto/w4m_HowToPerformXcmsPreprocessing_v02.pdf

Output files
------------

xset.RData: rdata.xcms.findchrompeaks format

    | (single) RData files that is necessary in the second step of the workflow "xcms.groupChromPeaks" must to be merged using "xcms.findChromPeaks Merger"
    | (zip) RData file that is necessary in the second step of the workflow "xcms.groupChromPeaks".

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

Changelog/News

39:e8d7395a70b2

                    </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-binSize*steps " />
                    <!-- index -->
                </section>
            </when>

            <!-- CentWaveWithPredIsoROIs -->

-----------
Description
-----------

This tool is used for preprocessing data from multiple LC/MS files (NetCDF, mzXML and mzData formats) using the xcms_ R package. It extracts ions from each sample independently, and using a statistical model, peaks are filtered and integrated.
A tutorial on how to perform xcms preprocessing is available here_.

.. _xcms: https://bioconductor.org/packages/release/bioc/html/xcms.html
.. _here: http://web11.sb-roscoff.fr/download/w4m/howto/w4m_HowToPerformXcmsPreprocessing_v02.pdf

Output files
------------

xset.RData: rdata.xcms.findchrompeaks format

    | (single) RData files that are necessary in the second step of the workflow "xcms.groupChromPeaks" - must be merged first using "xcms.findChromPeaks Merger"
    | (zip) RData file that is necessary in the second step of the workflow "xcms.groupChromPeaks".

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

Changelog/News