<tool id="abims_xcms_xcmsSet" name="xcms.xcmsSet" version="2.0.2">
    
    <description>Filtration and Peak Identification using xcmsSet function from xcms R package to preprocess LC/MS data for relative quantification and statistical analysis </description>
    
    <requirements>
        <requirement type="package" version="3.1.2">R</requirement>
        <requirement type="binary">Rscript</requirement>
        <requirement type="package" version="1.44.0">xcms</requirement>
        <requirement type="package" version="2.1">xcms_w4m_script</requirement>
    </requirements>
    
    <stdio>
        <exit_code range="1:" level="fatal" />
    </stdio>
    
    <command>
        xcms.r
        #if $inputs.input == "lib":
            library $__app__.config.user_library_import_dir/$__user_email__/$inputs.library
        #elif $inputs.input == "zip_file":
            zipfile $inputs.zip_file
        #end if

        xfunction xcmsSet
        ## profmethod $profmethod 
        nSlaves \${GALAXY_SLOTS:-1} method $methods.method 
        #if $methods.method == "centWave":
            ppm $methods.ppm
            peakwidth "c($methods.peakwidth)"
        #if $methods.options_scanrange.option == "show":
                scanrange "c($methods.options_scanrange.scanrange)"
            #end if 
            #if $methods.options_c.option == "show":
                mzdiff $methods.options_c.mzdiff
                snthresh $methods.options_c.snthresh
                integrate $methods.options_c.integrate
                noise $methods.options_c.noise
                prefilter "c($methods.options_c.prefilter)"
            #end if
        #elif $methods.method == "matchedFilter":
            step $methods.step
            fwhm $methods.fwhm
            #if $methods.options_m.option == "show":
                ## sigma "$methods.options_m.sigma"
                max $methods.options_m.max
                snthresh $methods.options_m.snthresh
                ## mzdiff $methods.options_m.mzdiff
                steps $methods.options_m.steps
                ## sleep $methods.options_m.sleep
            #end if
        #elif $methods.method == "MSW":
            snthr $methods.snthr
            nearbyPeak $methods.nearbyPeak
            winSize.noise $methods.winSize_noise
            amp.Th $methods.amp_Th
            scales "c($methods.scales)"
            SNR.method "$methods.SNR_method"
        #end if
        &amp;&amp; (mv xcmsSet.RData $xsetRData;
        mv sampleMetadata.tsv $sampleMetadata;
        mv TICs_raw.pdf $ticsRawPdf;
        mv BPCs_raw.pdf $bpcsRawPdf;
        mv xset.log $log);
        cat $log
    </command>
    
    <inputs>

        <conditional name="inputs">
            <param name="input" type="select" label="Choose your inputs method" >
                <option value="zip_file" selected="true">Zip file from your history containing your chromatograms</option>
                <option value="lib" >Library directory name</option>
            </param>
            <when value="zip_file">
                <param name="zip_file" type="data" format="no_unzip.zip" label="Zip file" />
             </when>
            <when value="lib">
                <param name="library" type="text" size="40" label="Library directory name" help="The name of your directory containing all your data" >
                <validator type="empty_field"/> 
            </param>
                </when>

        </conditional>

       
<!--
        <param name="profmethod" type="select" label="Method to use for profile generation (profmethod)" >
            <option value="bin" selected="true">bin</option>
            <option value="binlin">binlin</option>
            <option value="binlinbase">binlinbase</option>
            <option value="intlin">intlin</option>
        </param>
        <param name="nSlaves" type="integer" value="9" label="MPI-slaves CPU" help="number of MPI-slaves to use for parallel peak detection" />
-->
        <conditional name="methods">
            <param name="method" type="select" label="Extraction method for peaks detection" help="[method] See the help section below">
                <option value="centWave" >centWave</option>
                <option value="matchedFilter" selected="true">matchedFilter</option>
                <option value="MSW">MSW</option>
            </param>

            <!-- centWave Filter options -->
            <when value="centWave">
                <param name="ppm" type="integer" value="25" label="Max tolerated ppm m/z deviation in consecutive scans in ppm" help="[ppm]" />
                <param name="peakwidth" type="text" value="20,50" label="Min,Max peak width in seconds" help="[peakwidth]" />
                <conditional name="options_scanrange">
                    <param name="option" type="select" label="Scan range option " >
                        <option value="show">show</option>
                        <option value="hide" selected="true">hide</option>
                    </param>
                    <when value="show">
                        <param name="scanrange" type="text" value="" label="scanrange" help="scan range to process, for example (16,365)" >
                            <validator type="empty_field"/> 
                        </param>
                    </when>
                </conditional>
                        
                <conditional name="options_c">
                    <param name="option" type="select" label="Advanced options" >
                        <option value="show">show</option>
                        <option value="hide" selected="true">hide</option>
                    </param>
                    <when value="show">
                        <param name="snthresh" type="integer" value="10" label="Signal/Noise threshold" help="[snthresh] Signal to noise ratio cutoff" />
                        <param name="mzdiff" type="float" value="-0.001" label="Min m/z difference" help="[mzdiff] Min m/z difference for peaks with overlapping RT " />
                        <param name="integrate" type="select" label="peak limits method" help="[integrate]" >
                            <option value="1">peak limits based on smoothed 2nd derivative (less precise)</option>
                            <option value="2">peak limits based on real data (more sensitive to noise)</option>
                        </param>
                        <param name="prefilter" type="text" value="3,100" label="Prefilter step for the first phase" help="[prefilter] Separate by coma k,I. Mass traces are only retained if they contain at least ‘k’ peaks with intensity >= ‘I’"/>
                        <param name="noise" type="integer" value="0" label="Noise filter" help="[noise] optional argument which is useful for data that was centroided without any intensity threshold, centroids with intensity smaller than ‘noise’ are omitted from ROI detection"/>
                    </when>
                </conditional>
            </when>

        <!-- matched Filter options -->
            <when value="matchedFilter">
                <param name="step" type="float" value="0.01" label="Step size to use for profile generation" help="[step] The peak detection algorithm creates extracted ion base peak chromatograms (EIBPC) on a fixed step size" />
                <param name="fwhm" type="integer" value="30" label="Full width at half maximum of matched filtration gaussian model peak" help="[fwhm] Only used to calculate the actual sigma" />
                <conditional name="options_m">
                    <param name="option" type="select" label="Advanced options" >
                        <option value="show">show</option>
                        <option value="hide" selected="true">hide</option>
                    </param>
                    <when value="show">
<!--
                        <param name="sigma" type="hidden" value="fwhm/2.3548" label="sigma" help="standard deviation (fwhm/2.3548)" />
-->
                        <param name="max" type="integer" value="5" label="Maximum number of peaks per extracted ion chromatogram" help="[max]" />
                        <param name="snthresh" type="integer" value="10" label="Signal to noise ratio cutoff" help="[snthresh]" />
                        <param name="steps" type="integer" value="2" label="Number of steps to merge prior to filtration" help="[steps] The peak identification algorithm combines a given number of EIBPCs prior to filtration and peak detection, as defined by the steps argument" />
<!--
                        <param name="mzdiff" type="text" size="20" value="0.8-step*steps" label="m/z difference" help="min m/z difference for peaks with overlapping RT " />
-->
                    </when>
                </conditional>
            </when>

        <!-- MSW Filter options -->
            <when value="MSW">
                <param name="nearbyPeak" type="select" label="Determine whether to include the nearby small peaks of major peaks" help="[nearbyPeak]" >
                    <option value="TRUE">TRUE</option>
                    <option value="FALSE">FALSE</option>
                </param>
                <param name="winSize_noise" type="integer" value="500" label="The local window size to estimate the noise level" help="[winSize.noise]" />
                <param name="snthr" type="integer" value="3" label="SNR (Signal to Noise Ratio) threshold" help="[snthr]" />
                <param name="amp_Th" type="float" value="0.002" label="Minimum required relative amplitude of the peak" help="[amp.Th] Ratio to the maximum of CWT coefficients" />
                <param name="scales" type="text" value="seq(1,22,3)" label="Scales for the Continuous Wavelet Transform (CWT)" help="[scales] Scales are linked to the width of the peaks that are to be detected. Tape as indicaded seq('n,n,n') or c(n,n) : seq(from, to, by steps), c - linear vector " />
                <param name="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>
    </inputs>
    
    <outputs>
        <data name="xsetRData" format="rdata.xcms.raw" label="xset.RData" />
        <data name="sampleMetadata" format="tabular" label="sampleMetadata.tsv" />
        <data name="ticsRawPdf"   format="pdf" label="xset.TICs_raw.pdf" />
        <data name="bpcsRawPdf"   format="pdf" label="xset.BPCs_raw.pdf" />
        <data name="log" format="txt" label="xset.log.txt" />
    </outputs>
    
    <tests>
        <test>
            <param name="inputs.input" value="zip_file" />
            <param name="inputs.zip_file" value="sacuri.zip" />
            <param name="methods.method" value="matchedFilter" />
            <param name="methods.step" value="0.01" />
            <param name="methods.fwhm" value="4" />
            <param name="methods.options_m.option" value="show" />
            <param name="methods.options_m.max" value="50" />
            <param name="methods.options_m.snthresh" value="1" />
            <param name="methods.options_m.steps" value="2" />
            <output name="xsetRData" file="xset.RData" />
            <output name="sampleMetadata" file="sampleMetadata.tsv" />
            <output name="ticsRawPdf" file="xset.TICs_raw.pdf" />
            <output name="bpcsRawPdf" file="xset.BPCs_raw.pdf" />
            <output name="log" file="xset.log.txt" />
        </test>
    </tests>
    
    <help>

.. class:: infomark

**Authors**  Colin A. Smith csmith@scripps.edu, Ralf Tautenhahn rtautenh@gmail.com, Steffen Neumann sneumann@ipb-halle.de, Paul Benton hpaul.benton08@imperial.ac.uk and Christopher Conley cjconley@ucdavis.edu 

.. class:: infomark

**Galaxy integration** ABiMS TEAM - UPMC/CNRS - Station biologique de Roscoff and Yann Guitton yann.guitton@univ-nantes.fr - part of Workflow4Metabolomics.org [W4M]

 | Contact support@workflow4metabolomics.org for any questions or concerns about the Galaxy implementation of this tool.

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

============
Xcms.xcmsSet
============

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

This tool is used for preprocessing analyte data from multiple LC/MS files (formats NetCDF, mzXML and mzData). 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_.

.. _here: http://web11.sb-roscoff.fr/download/w4m/howto/w4m_HowToPerformXcmsPreprocessing_v02.pdf


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

**Upstream tools**

========================= ================= ======= =========
Name                      output file       format  parameter
========================= ================= ======= =========
NA                        NA                zip     NA       
========================= ================= ======= =========


**Downstream tools**

+---------------------------+--------------------+-----------------+
| Name                      | Output file        | Format          |
+===========================+====================+=================+
|xcms.group                 | xset.RData         | rdata.xcms.raw  |
+---------------------------+--------------------+-----------------+
|PCA ellipsoid by factors   | sampleMetadata.tsv | Tabular         |
+---------------------------+--------------------+-----------------+
|Anova                      | sampleMetadata.tsv | Tabular         |
+---------------------------+--------------------+-----------------+


**Example of a metabolomic workflow**

.. image:: XCMS_Galaxy_workflow.png


------

.. class:: infomark 

The output file is an xset.RData file. You can continue your analysis using it in **xcms.group** tool.

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



-----------
Input files
-----------

+---------------------------+------------+
| Parameter : num + label   |   Format   |
+===========================+============+
| 1 : Choose your inputs    |   zip      |
+---------------------------+------------+

**Choose your inputs**

You have two methods for your inputs:

    | Zip file (recommended): You can put a zip file containing your inputs: myinputs.zip (containing all your conditions as sub-directories).
    | library folder: You must specify the name of your "library" (folder) created within your space project (for example: /projet/externe/institut/login/galaxylibrary/yourlibrary). Your library must contain all your conditions as sub-directories.

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

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

**Matched Filter**

    | One parameter to consider is the Gaussian model peak width used for matched filtration,an integral part of the peak detection algorithm. 
    | For a discussion of how model peak width affects the signal to noise ratio, see Danielsson et al. (2002).


**cent Wave**

    | This algorithm is most suitable for high resolution LC/{TOF,OrbiTrap,FTICR}-MS data in centroid mode.
    | 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.

**MSW**

    | Wavelet based, used for direct infusion data. Continuous wavelet transform (CWT) can be used to locate chromatographic peaks on different scales.
    | If you wish to have more details about the other parameters, you can read the following documents:
    | -Example of preprocessing data with XCMS : http://www.bioconductor.org/packages/2.12/bioc/vignettes/xcms/inst/doc/xcmsPreprocess.pdf
    | -Details and explanations for all the parameters of XCMS package: http://www.bioconductor.org/packages/release/bioc/manuals/xcms/man/xcms.pdf


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

xset.TICs_raw.pdf

    | "Total Ion Chromatograms" graph in pdf format.

xset.BPCs_raw.pdf

    | "Base Peak Chromatograms" graph in pdf format with each class samples opposed.

sampleMetadata.tsv

    | 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.raw format

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

.. class:: infomark 

The output file is an xset.RData file. You can continue your analysis using it in **xcms.group** tool.

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

---------------
Working example
---------------

Input files
-----------

    | zip_file -> **sacuri.zip**

Parameters
----------

    | Method -> **matchedFilter**
    | step   -> **0.01**
    | fwhm   -> **4** 
    | Advanced option -> **show**
    | max: -> **50**
    | snthresh -> **1**
    | steps -> **2**


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

    | **1) xset.RData: RData file**

    | **2) Example of a sampleMetadata.tsv  :**


+---------------------------+------------+---------+
| sampleMetadata            |   class    | polarity|
+===========================+============+=========+
|HU_neg_017                 |   bio      |negative |
+---------------------------+------------+---------+
|HU_neg_028                 |   bio      |negative |
+---------------------------+------------+---------+
|HU_neg_034                 |   bio      |negative |
+---------------------------+------------+---------+
|Blanc04                    |   blank    |negative |
+---------------------------+------------+---------+
|Blanc06                    |   blank    |negative |
+---------------------------+------------+---------+
|Blanc09                    |   blank    |negative |
+---------------------------+------------+---------+



    | **3) Example of xset.TICs_raw.pdf (Total Ion Chromatograms) :**

.. image:: xcms_tics.png


    </help>


    <citations>
        <citation type="doi">10.1021/ac051437y</citation>
        <citation type="doi">10.1093/bioinformatics/btu813</citation>
    </citations>

</tool>