<tool id="abims_xcms_xcmsSet" name="xcms findChromPeaks (xcmsSet)" version="@WRAPPER_VERSION@.0">
    <description>Chromatographic peak detection</description>

    <macros>
        <import>macros.xml</import>
        <import>macros_xcms.xml</import>
    </macros>

    <expand macro="requirements"/>
    <expand macro="stdio"/>

    <command><![CDATA[
        @COMMAND_RSCRIPT@/xcms_xcmsSet.r

        image '$image'

        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":
            @COMMAND_CENTWAVE@
            ## List of regions-of-interest (ROI)
            #set $sectionROI = $methods.CentWaveAdv.CentWaveAdvROI
            @COMMAND_CENTWAVEADVROI@
        #elif $methods.method == "CentWavePredIso":
            @COMMAND_CENTWAVE@
            ## List of regions-of-interest (ROI)
            #set $sectionROI = $methods.CentWaveAdvROI
            @COMMAND_CENTWAVEADVROI@
            snthreshIsoROIs $sectionROI.snthreshIsoROIs
            maxCharge $sectionROI.maxCharge
            maxIso $sectionROI.maxIso
            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
            steps $methods.MatchedFilterAdv.steps
            mzdiff $methods.MatchedFilterAdv.mzdiff
        #elif $methods.method == "MSW":
            snthresh $methods.snthresh
            verboseColumns $methods.verboseColumns
            scales "c($methods.scales)"
            nearbyPeak $methods.nearbyPeak
            ampTh $methods.ampTh
        #end if

        @COMMAND_FILE_LOAD@

        @COMMAND_LOG_EXIT@
    ]]></command>

    <inputs>

        <param name="image" type="data" format="rdata.msnbase.raw,rdata" label="@INPUT_IMAGE_LABEL@" help="@INPUT_IMAGE_HELP@ from MSnbase readMSData" />

        <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="CentWavePredIso">CentWaveWithPredIsoROIs - performs a two-step centWave-based chromatographic peak detection</option>
                <option value="MSW">MSW - single-spectrum non-chromatography MS data peak detection</option>
            </param>

            <!-- CentWave -->
            <when value="CentWave">
                <expand macro="input_centwave"/>
                <section name="CentWaveAdv" title="Advanced Options" expanded="False">
                    <expand macro="input_centwaveAdv"/>
                    <section name="CentWaveAdvROI" title="List of regions-of-interest (ROI)" expanded="False">
                        <expand macro="input_centwaveAdvROI"  optional="true"/>
                    </section>
                </section>
            </when>

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

            <!-- CentWaveWithPredIsoROIs -->
            <when value="CentWavePredIso">
                <expand macro="input_centwave"/>
                <section name="CentWaveAdv" title="Advanced Options" expanded="False">
                    <expand macro="input_centwaveAdv"/>
                </section>
                <section name="CentWaveAdvROI" title="List of regions-of-interest (ROI)" expanded="True">
                    <expand macro="input_centwaveAdvROI" optional="true" />
                    <param argument="snthreshIsoROIs" type="float" value="6.25" label="Signal to noise ratio cutoff" help="used in the second centWave run to identify peaks for predicted isotope ROIs." />
                    <param argument="maxCharge" type="integer" value="3" label="Maximal isotope charge" help="Isotopes will be defined for charges ‘1:maxCharge’." />
                    <param argument="maxIso" type="integer" value="5" label="Number of isotope peaks that should be predicted for each peak identified in the first centWave run" />
                    <param argument="mzIntervalExtension" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Is the mz range for the predicted isotope ROIs should be extended to increase detection of low intensity peaks" />
                    <param argument="polarity" type="select" label="Polarity of the data">
                        <option value="unknown">unknown</option>
                        <option value="positive">positive</option>
                        <option value="negative">negative</option>
                    </param>
                </section>
            </when>

            <!-- MSW -->
            <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 -->
                <!-- peakThr -->
                <!-- tuneIn -->
                <!---@TODO <param argument="SNR_method" type="text" value="data.mean" label="SNR (Signal to Noise Ratio) method" help="[SNR.method] Method to estimate noise level. Currently, only 95 percentage quantile is supported." />-->
            </when>
        </conditional>

        <expand macro="input_file_load"/>
    </inputs>

    <outputs>
        <data name="xsetRData" format="rdata.xcms.findchrompeaks" label="${image.name.rsplit('.',1)[0]}.xset.RData" from_work_dir="xcmsSet.RData" />
        <data name="log" format="txt" label="${image.name.rsplit('.',1)[0]}.xset.log.txt" from_work_dir="log.txt" />
    </outputs>

    <tests>

        <!--<test>
            <param name="image" value="faahKO.raw.Rdata" ftype="rdata" />
            <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" />-->
                <!-- DISABLE: just for testing the arguments
                <section name="CentWaveAdv">
                    <section name="CentWaveAdvROI">
                        <param name="roiList" value="roiList.txt" ftype="tabular" />
                    </section>
                </section>-->
            <!--</conditional>
            <expand macro="test_file_load_zip"/>
            <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>
            <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>
            <expand macro="test_file_load_single_ko15"/>
            <assert_stdout>
                <has_text text="ppm: 25" />
                <has_text text="peakwidth: 20, 50" />
                <has_text text="object with 1 samples" />
                <has_text text="Time range: 2506.1-4471.7 seconds (41.8-74.5 minutes)" />
                <has_text text="Mass range: 200.2-600 m/z" />
                <has_text text="Peaks: 2262 (about 2262 per sample)" />
                <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>
            <assert_stdout>
                <has_text text="object with 1 samples" />
                <has_text text="Time range: 2521.7-4477.9 seconds (42-74.6 minutes)" />
                <has_text text="Mass range: 200.1-600 m/z" />
                <has_text text="Peaks: 2408 (about 2408 per sample)" />
                <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>
            <assert_stdout>
                <has_text text="object with 1 samples" />
                <has_text text="Time range: 2517-4473.2 seconds (42-74.6 minutes)" />
                <has_text text="Mass range: 200.2-599.8 m/z" />
                <has_text text="Peaks: 2278 (about 2278 per sample)" />
                <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>
            <assert_stdout>
                <has_text text="object with 1 samples" />
                <has_text text="Time range: 2521.7-4468.5 seconds (42-74.5 minutes)" />
                <has_text text="Mass range: 200.3-600 m/z" />
                <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">
                    <param name="roiList" value="roiList.txt" ftype="tabular" />
                </section>
            </conditional>
            <assert_stdout>
                <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>
            <assert_stdout>
                <has_text text="snthresh: 4" />
                <has_text text="verboseColumns: TRUE" />
            </assert_stdout>
        </test>
        -->
        <!-- DISABLE FOR TRAVIS
        No more test-data/sacuri_dir_root.zip
        <test>
            <param name="image" value="sacuri_dir_root.zip"  ftype="zip" />
            <conditional name="methods">
                <param name="method" value="MatchedFilter" />
                <param name="step" value="0.01" />
                <param name="fwhm" value="4" />
                <conditional name="options_m">
                    <param name="option" value="show" />
                    <param name="max" value="50" />
                    <param name="snthresh" value="1" />
                    <param name="steps" value="2" />
                </conditional>
            </conditional>
            <assert_stdout>
                <has_text text="object with 4 samples" />
                <has_text text="Time range: 0.7-1139.7 seconds (0-19 minutes)" />
                <has_text text="Mass range: 50.0021-999.9863 m/z" />
                <has_text text="Peaks: 59359 (about 14840 per sample)" />
                <has_text text="Peak Groups: 0" />
                <has_text text="Sample classes: bio, blank" />
            </assert_stdout>
        </test>
        -->
        <!--  DISABLE FOR TRAVIS
        No more test-data/sacuri_current_root.zip
        <test>
            <param name="image" value="sacuri_current_root.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="object with 4 samples" />
                <has_text text="Time range: 3.5-1139.2 seconds (0.1-19 minutes)" />
                <has_text text="Mass range: 57.9756-593.4086 m/z" />
                <has_text text="Peaks: 1535 (about 384 per sample)" />
                <has_text text="Peak Groups: 0" />
                <has_text text="Sample classes: bio, blank" />
            </assert_stdout>
        </test>
        -->
    </tests>

    <help><![CDATA[

@HELP_AUTHORS@

===================
xcms findChromPeaks
===================

-----------
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


-----------------
Workflow position
-----------------

**Upstream tools**

========================= ================= ==============================
Name                      Output file       Format
========================= ================= ==============================
MSnbase.readMSData        ``*``.raw.RData   rdata.msnbase.raw
========================= ================= ==============================


**Downstream tools**

==================================== ======================== =========================
Name                                 Output file              Format
==================================== ======================== =========================
xcms.findChromPeaks Merger (single)  ``*``.raw.xset.RData     rdata.xcms.findchrompeaks
------------------------------------ ------------------------ -------------------------
xcms.groupChromPeaks (zip)           ``*``.raw.xset.RData     rdata.xcms.findchrompeaks
==================================== ======================== =========================


**Example of a metabolomic workflow**

.. image:: xcms_xcmsset_workflow.png

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

----------
Parameters
----------

Extraction method for peaks detection
-------------------------------------

**MatchedFilter**

    | The matchedFilter algorithm identifies peaks in the chromatographic time domain as described in [Smith 2006]. The intensity values are binned by cutting The LC/MS data into slices (bins) of a mass unit (‘binSize’ m/z) wide. Within each bin the maximal intensity is selected. The chromatographic peak detection is then performed in each bin by extending it based on the ‘steps’ parameter to generate slices comprising bins ‘current_bin - steps +1’ to ‘current_bin + steps - 1’. Each of these slices is then filtered with matched filtration using a second-derative Gaussian as the model peak shape. After filtration peaks are detected using a signal-to-ratio cut-off. For more details and illustrations see [Smith 2006].
    | See the MatchedFilter_manual_

**CentWave**

    | The centWave algorithm perform peak density and wavelet based chromatographic peak detection for high resolution LC/MS data in centroid mode [Tautenhahn 2008].
    | Due to the fact that peak centroids are used, a binning step is not necessary.
    | The method is capable of detecting close-by-peaks and also overlapping peaks. Some efforts are made to detect the exact peak boundaries to get precise peak integrals.
    | See the CentWave_manual_

**CentWaveWithPredIsoROIs**

    | This method performs a two-step centWave-based chromatographic peak detection: in a first centWave run peaks are identified for which then the location of their potential isotopes in the mz-retention time is predicted. A second centWave run is then performed on these regions of interest (ROIs). The final list of chromatographic peaks comprises all non-overlapping peaks from both centWave runs.
    | See the CentWaveWithPredIsoROIs_manual_

**MSW**

    | Wavelet based, used for direct infusion data. Continuous wavelet transform (CWT) can be used to locate chromatographic peaks on different scales.
    | See the MSW_manual_

.. _MatchedFilter_manual: https://rdrr.io/bioc/xcms/man/findChromPeaks-matchedFilter.html#heading-2
.. _CentWave_manual: https://rdrr.io/bioc/xcms/man/findChromPeaks-centWave.html#heading-2
.. _CentWaveWithPredIsoROIs_manual: https://rdrr.io/bioc/xcms/man/findChromPeaks-centWaveWithPredIsoROIs.html#heading-2
.. _MSW_manual: https://rdrr.io/bioc/xcms/man/findPeaks-MSW.html#heading-2

@HELP_XCMS_MANUAL@

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

.. _News: https://bioconductor.org/packages/release/bioc/news/xcms/NEWS

**Version 3.4.4.0 - 08/02/2019**

- UPGRADE: upgrade the xcms version from 3.0.0 to 3.4.4 (see XCMS News_)


**Version 3.0.0.0 - 08/03/2018**

- UPGRADE: upgrade the xcms version from 1.46.0 to 3.0.0. So refactoring of a lot of underlying codes and methods. Some parameters may have been renamed.

- CHANGE: xcms.findChromPeaks no longer read the raw data. You have to run MSnbase readMSData first.

- NEW: a bunch of new options: Spectra Filters (previously scanrange), CentWave.(mzCenterFun, fitgauss, verboseColumns), MatchedFilter.(sigma, impute, baseValue, max), MSW.(verboseColumns), ...

- NEW: new Filters for Spectra

- NEW: new methods: CentWaveWithPredIsoROIs

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

- IMPROVEMENT: the advanced options are now in sections. It will allow you to access to all the parameters and to know their default values.

- IMPROVEMENT: the tool "should" be now more flexible in term of file naming: it "should" accept space and comma. But don't be too imaginative :)

- CHANGE: removing of the TIC and BPC plots. You can new use the dedicated tool "xcms plot chromatogram"


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

- BUGFIX: To avoid issues with accented letter in the parentFile tag of the mzXML files, we changed a hidden mechanim to LC_ALL=C


**Version 2.1.0 - 22/02/2017**

- NEW: The W4M tools will be able now to take as input a single file. It will allow to submit in parallel several files and merge them afterward using "xcms.xcmsSet Merger" before "xcms.group".

- BUGFIX: the default value of "matchedFilter" -> "Step size to use for profile generation" which was of 0.01 have been changed to fix with the XMCS default values to 0.1


**Version 2.0.11 - 22/12/2016**

- BUGFIX: propose scanrange for all methods


**Version 2.0.10 - 22/12/2016**

- BUGFIX: when having only one group (i.e. one folder of raw data) the BPC and TIC pdf files do not contain any graph


**Version 2.0.9 - 06/07/2016**

- UPGRADE: upgrade the xcms version from 1.44.0 to 1.46.0


**Version 2.0.8 - 06/04/2016**

- TEST: refactoring to pass planemo test using conda dependencies


**Version 2.0.7 - 10/02/2016**

- BUGFIX: better management of errors. Datasets remained green although the process failed

- BUGFIX/IMPROVEMENT: New checking steps around the imported data in order to raise explicte error message before or after launch XCMS: checking of bad characters in the filenames, checking of the XML integrity and checking of duplicates which can appear in the sample names during the XCMS process because of bad characters

- BUGFIX/IMPROVEMENT: New step to check and delete bad characters in the XML: accented characters in the storage path of the mass spectrometer

- UPDATE: refactoring of internal management of inputs/outputs

- TEST: refactoring to feed the new report tool


**Version 2.0.2 - 18/01/2016**

- BUGFIX: Some zip files were tag as "corrupt" by R. We have changed the extraction mode to deal with thoses cases.


**Version 2.0.2 - 09/10/2015**

- BUGFIX: Some users reported a bug in xcms.xcmsSet. The preprocessing stops itself and doesn't import the whole dataset contained in the zip file without warning. But meanwhile, please check your samplemetadata dataset and the number of rows.


**Version 2.0.2 - 02/06/2015**

- NEW: The W4M workflows will now take as input a zip file to ease the transfer and to improve dataset exchange between tools and users. (See How_to_upload). The previous "Library directory name" is still available but we invite user to switch on the new zip system as soon as possible.

- IMPROVEMENT: new datatype/dataset formats (rdata.xcms.raw, rdata.xcms.group, rdata.xcms.retcor ...) will facilitate the sequence of tools and so avoid incompatibility errors.

- IMPROVEMENT: parameter labels have changed to facilitate their reading.

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