<!--
    wl-02-11-2017, Thu: commence
    wl-25-11-2017, Sat: The first working version
    wl-28-11-2017, Tue: deal with composite files
    wl-25-01-2018, Thu: remove 'offset' and add more help from Zoe.
    wl-14-02-2018, Wed: More modifications:
      1) change text file format from csv to tsv
      2) more control for output
    wl-06-04-2019, Sat: add more tests for planemo. 
-->
<tool id="massPix" name="massPix" version="0.1.0">
  <description>
    Processes high resolution mass spectrometry imaging data,
    performs multivariate statistics (PCA, clustering) and lipid
    identification.
  </description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements" />
  <expand macro="stdio" />

  <command>
    <![CDATA[
      ln -s '${imzML_file.extra_files_path}/imzml' data.imzml &&
      ln -s '${imzML_file.extra_files_path}/ibd' data.ibd &&

      Rscript '${__tool_directory__}/massPix.R'
      --imzML_file data.imzml

      --process '$process.process_selector'      
      #if $process.process_selector =="TRUE":

          ## Making library
          --ionisation_mode '$process.make_library.ionisation_mode'
          --fixed '$process.make_library.fixed'
          --fixed_FA '$process.make_library.fixed_FA'
          
          ## mz_extractor
          --thres_int '$process.mz_extractor.thres_int' 
          --thres_low '$process.mz_extractor.thres_low'
          --thres_high '$process.mz_extractor.thres_high'
          
          ## peak_piucker_bin
          --bin_ppm '$process.peak_piucker_bin.bin_ppm'
          
          ## subset_image
          --percentage_deiso '$process.subset_image.percentage_deiso'
          
          ## filter
          --steps '$process.filter.steps'
          --thres_filter '$process.filter.thres_filter'
          
          ## deisotope
          --ppm '$process.deisotope.ppm'
          --no_isotopes '$process.deisotope.no_isotopes'
          --prop_1 '$process.deisotope.prop_1'
          --prop_2 '$process.deisotope.prop_2'
          --search_mod '$process.deisotope.search_mod'
          ##--mod '$process.deisotope.mod'
          ## wl-25-11-2017, Sat: Must add single quotes here since mod
          ##   content includes parentheses. Otherwise error:
          ##   syntax error near unexpected token `('

        #set $NL_var = 'F'
        #set $label_var = 'F'
        #set $desat_var = 'F'
        #set $oxidised_var = 'F'

        #if 'nl' in str($process.deisotope.mod): 
            #set $NL_var = 'T'
        #elif 'lab' in str($process.deisotope.mod):
            #set $label_var = 'T'
        #elif 'des' in str($process.deisotope.mod): 
            #set $desat_var = 'T'
        #elif 'ox' in str($process.deisotope.mod): 
            #set $oxidised_var = 'T'
        #end if

          --mod "c(NL = $NL_var, label = $label_var, oxidised = $oxidised_var, desat = $desat_var)"

          ## annotate
          --ppm_annotate '$process.annotate.ppm_annotate'
          
          ## normalise
          --norm_type '$process.normalise.norm_type.norm_type_selector'
          #if $process.normalise.norm_type.norm_type_selector == 'standards':
            --standards '$process.normalise.norm_type.standards'
          #end if

          ## save processed image 
          --image_out '$image_out'
          #if $process.rdata: 
            --rdata_out '$rdata_out'
          #end if
      #else:
          --image_file '$process.image_file'
      #end if

      ## plot
      --scale '$plot.scale'
      --nlevels '$plot.nlevels'
      --res_spatial '$plot.res_spatial'
      --rem_outliers '$plot.rem_outliers'
      --summary '$plot.summary'
      --title '$plot.title'

      --pca '$pca.pca_selector'
      #if $pca.pca_selector =="TRUE":
          --pca_out '$pca_out'    
          --scale_type '$pca.scale_type'
          --transform '$pca.transform'
          --PCnum '$pca.PCnum'
          --loading '$pca.loading'
          #if $pca.loading:
            --loading_out '$loading_out'
          #end if  
      #end if

      --slice $slice_selector
      #if $slice_selector:
          --row '$row'
          --slice_out '$slice_out'
      #end if

      --clus '$cluster.cluster_selector'
      #if $cluster.cluster_selector =="TRUE":
          --clus_out '$clus_out'
          --cluster_type '$cluster.cluster_type'
          --clusters '$cluster.clusters'
          --intensity '$cluster.intensity'
          #if $cluster.intensity:
            --intensity_out '$intensity_out'
          #end if  
      #end if
    ]]>
  </command>

  <!-- =============================================================== -->
  <inputs>

    <param name="imzML_file" type="data" format="imzml" 
           label="Choose an imzml composite file"
           help="imzml file contains imaging meta data. The imaging binary 
                 data file (*.ibd) contains the mass spectral data. The two
                 files must be uploaded as an 'imzml' 'composite' data type 
                 via 'Get Data'. " />

        <conditional name="process">
            <param label="Process mass spectrometry imaging data"
                 name="process_selector"
                 type="select"
                 help="Choose if you want to process MSI data or only visualise
                       processed MSI data." >
                <option value="TRUE" selected="True">perform processing</option>
                <option value="FALSE">visualisation of processed file</option>
            </param>

            <when value="TRUE">

        <!-- ########################################################### -->
        <section name="make_library" title="Making library" > 

          <param name="ionisation_mode" type="select"
                 label="Specify ionisation mode"
                 help="Choose 'positive' or 'negative', will determine
                       which lipid classes are in database"
                 display="radio">
                <option value="positive" selected="True">positive</option>
                <option value="negative">negative</option>
          </param>

          <param name="fixed" type="boolean" 
                 truevalue="TRUE" falsevalue="FALSE" 
                 checked="false" label="SN position fixed or not"
                 help="Defines if one of the SN positions is fixed, default
                       is false." />

          <param name="fixed_FA" type="float" value="16"
                 label="Fixed FA"
                 help="Defines the name of the fixed FA eg 16, 18.1, 20.4." />
        </section>

        <!-- ########################################################### -->
        <section name="mz_extractor" title="Extract m/z and pick peaks" >

          <param name="thres_int" type="integer" value="100000"
                 label="Intensity threshold"
                 help="Defines the intensity threshold, above which ions are 
                       retained"/>
          
          <param name="thres_low" type="integer" value="200"
                 label="Minumum m/z threshold"
                 help="Defines the minimum m/z threshold, above which ions 
                       will be retained"/>

          <param name="thres_high" type="integer" value="1000"
                 label="Maximum m/z threshold"
                 help="Defines the maximum m/z threshold, below which ions 
                       will be retained"/>
          
        </section>

        <!-- ########################################################### -->
        <section name="peak_piucker_bin" title="Bin all m/zs by ppm bucket">
          
          <param name="bin_ppm" type="integer" value="10"
                 label="Bin width (ppm)"
                 help="Mass accuracy for binning between spectra. Suggest
                       starting with 10 ppm bin width for data acquired with mass
                       resolving power 60,000 at m/z 400; increase/decrease with
                       lower/higher resolving power, respectively. Used to group
                       common ions across all spectra (pixels) where ions are
                       measured with slightly different m/z."  /> 
         </section>

        <!-- ########################################################### -->
        <section name="subset_image"
                 title="Generate subset of first image file to improve speed
                        of deisotoping">

          <param name="percentage_deiso" type="integer" value="3"
                 label="Proportion of deisotoping"
                 help="Defines the proportion of total pixels to select,
                       at random from the first file to produce a subset
                       of the image"/>
        </section>

        <!-- ########################################################### -->
        <section name="filter"
                 title="Filter to a matrix subset that includes
                        variables above a threshold of missing values">
          <param name="steps" type="float" value="0.05"
                 min="0" max="1"
                 label="Steps for filtering"
                 help="This produces a sequence of values between 0 and 1 
                       that defines the thresholds of missing values to test. 
                       Do not change this value from 0.05 but rather change 
                       Threshold for filtering to adjust missing value tolerance." />
          
          <param name="thres_filter" type="integer" value="11"
                 min="1" max="21"
                 label="Threshold for filtering"
                 help="Defines threshold for proportion of missing values
                       (this is the step number, not the actual proportion).
                       Range is 1-21, where each step size corresponds to an increase 
                       in 0.05 (5 %) missing values allowed. For example: 
                       Step 1:  0 threshold - no missing values allowed (feature must 
                       be present in at least 100% pixels)
                       Step 6: 0.25 threshold -25 % missing values allowed (feature 
                       must be present in at least 75 % pixels)
                       Step 11: 0.5 threshold - 50 % missing values allowed (feature 
                       must be present in at least 50 % pixels)
                       Step 16: 0.75 threshold - 75 % missing values allowed (feature 
                       must be present in at least 25 % pixels)
                       Step 21:  1 threshold - 100 % missing values allowed (feature 
                       must be present in at least 0 % pixels)."
                 />
        </section>

        <!-- ########################################################### -->
        <section name="deisotope"
                 title="Perform deisotoping on a subset of the image">
          
          <param name="ppm" type="integer" value="3" label="Tolerance (ppm)"
                 help="Tolerance (ppm) within which mass of isotope must
                       be within"/>

          <param name="no_isotopes" type="integer" value="2"
                 min="1" max="2"
                 label="Number of isotopes"
                 help="Number of isotopes to consider (1 or 2)"/>

          <param name="prop_1" type="float" value="0.9" min="0" max="1"
                 label="First Proportion"
                 help="Proportion of monoisotope intensity the 1st isotope
                       intensity must not exceed"/>

          <param name="prop_2" type="float" value="0.5" min="0" max="1"
                 label="Second proportion"
                 help="Proportion of monoisotope intensity the 2nd isotope
                       intensity must not exceed"/>
          
          <param name="search_mod" type="boolean" 
                 truevalue="TRUE" falsevalue="FALSE" checked="true" 
                 label="Search modifications"
                 help="Search modifications T/F."/>


          <param name="mod" type="select"
                 optional="True"
                 display="checkboxes"
                 multiple="True"
                 label="Specify modifications to search"
                 help="Modifications to search eg.neutral loss of
                       head group or water; 13C palmitate lablled;
                       1 to 4 additional desaturations; oxidised">
             <option value="nl" selected="True">Neutral loss</option>
             <option value="lab">13C palmitate labelled</option>
             <option value="des">1 to 4 additional desaturations</option>
             <option value="ox">Oxidised</option>
        </param>

        </section>

        <!-- ########################################################### -->
        <section name="annotate"
                 title="Perform putative annotation on deisotoped image">
          <param name="ppm_annotate" type="integer" value="10"
                 label="Specify ppm threshold for annotation"
                 help="Defines ppm threshold for which |observed m/z -
                       theoretical m/z| must be less than for annotation to be
                       retained. Suggest to use same mass tolerance 
                       as bin width." /> 
        </section>

        <!-- ########################################################### -->
        <section name="normalise" title="Normalise image">
          <conditional name="norm_type">

            <param name="norm_type_selector" type="select"
                   label="Select a method for normalisation"
                   help="Mode of normalisation" >
              <option value="TIC" selected="true">Total Ion Current</option>
              <option value="standards">Standard</option>
              <option value="median">Median</option>
              <option value="none">None</option>
            </param>
            <when value="standards">
              <!-- FIXME: not sure 'text' is the right type for standards -->
              <!-- wl-25-11-2017, Sat: R has a class of NULL. Convert text
               "NULL" to NULL in R: as.null("NULL") -->
              <param name="standards" type="text" value="NULL"
                     label="Specify vector of row"
                     help="Vector of row indices corresponding to variables
                           that are standards. The input format should follow the 
                           example: 'c(1,3:21,35)' where ':' stands for the range. 
                           If the input is 'NULL', all rows will be used."/>
             </when> 
             <when value="TIC" />
             <when value="median" />
             <when value="none" />

           </conditional>
         </section>
       
         <param name="rdata" type="boolean" truevalue="TRUE" 
                falsevalue="FALSE" checked="true"
                label="Save all R running results"
                help="Save all running results for inspection" />

       </when>

      <when value="FALSE">
        <param name="image_file" format="tabular" type="data"
               label="Choose processed data"
               help="Choose processed data file for PCA or clustering analysys" />
      </when>
      
    </conditional>

    <section name="plot" title="Specify plot parameters">
          <param name="scale" type="integer" value="100"
                 label="Specify scale range"
                 help="Range of scale that intensity values will be
                       scaled to."/>

          <param name="nlevels" type="integer" value="50"
                 label="Specify Graduations"
                 help="Graduations of colour scale."/>

          <param name="res_spatial" type="integer" value="50"
                 label="Specify spatial resolution"
                 help="Spatial resolution of image" />

          <!-- FIXME: Problem: mix str and boolean. Change as boolean.  -->
          <param name="rem_outliers" type="boolean" truevalue="TRUE"
                 falsevalue="FALSE" checked="true"
                 label="Remove outliers or not"
                 help="Remove intensities that are outliers or not" />

          <param name="summary" type="boolean" 
                 truevalue="TRUE" falsevalue="FALSE"
                 checked="false"
                 label="Give summary information or not"
                 help="Summary information with boxplot and histogram"/>

          <param name="title" type="boolean" 
                 truevalue="TRUE" falsevalue="FALSE"
                 checked="true"
                 label="Show plot title or not"
                 help="Provide plot title for outlier handling."/>
    </section>
    
    <conditional name="pca">
        <param name="pca_selector"
             type="select"
             label="Generate PCA plot"
             help="Select generating a PCA plot or not" >
                <option value="TRUE" selected="True">Generate PCA plot</option>
                <option value="FALSE">no PCA plot</option>
            </param>

            <when value="TRUE">
                  <param name="scale_type" type="select"
                         label="Select a method for scaling"
                         help="Mode of scaling. Valid argument: center, 
                               center and pareto, pareto and none">
                    <option value="cs" selected="true">Center and Pareto</option>
                    <option value="c">Center</option>
                    <option value="pareto">Pareto</option>
                    <option value="none">None</option>
                  </param>

                  <param name="transform" type="boolean" 
                         truevalue="TRUE" falsevalue="FALSE" checked="false"
                         label="Transformation or not"
                         help="Log transform data T/F"/>

                  <param name="PCnum" type="integer" value="5" label="Specify PCs"
                         help="Number of PCs to consider" /> 

                  <param name="loading" type="boolean" 
                         truevalue="TRUE" falsevalue="FALSE" checked="true"
                         label="Save loading values"
                         help="Save loading values for inspection."/>
            </when>

            <when value="FALSE" />
        </conditional>

        <param name="slice_selector" type="boolean" 
               truevalue="TRUE" falsevalue="FALSE" checked="true"
               label="Plot ion slice or not"
               help="Make ion slice if requested" >
        </param>

        <param name="row" type="integer" value="12"
             label="For ion slice plotting: specify row"
             help="Row number to plot - this can be determined by 
                   opening the processed image data file."
             optional="True"/>
    
    <conditional name="cluster"> 
        <param name="cluster_selector" type="select" 
               label="Perform clustering or not"
               help="Perform clustering or not" >
            <option value="TRUE" selected="True">Perform clustering</option>
            <option value="FALSE">No clustering</option>
        </param>

      <when value="TRUE">
          <param name="cluster_type" type="select"
                 label="Select a clustering method"
                 help="Currently only 'kmeans' supported" >
            <option value="kmeans" selected="true">k-means</option>
          </param>

          <param name="clusters" type="integer" value="5"
                 label="Specify cluster numbers"
                 help="Number of clusters to use" />

          <param name="intensity" type="boolean" 
                 truevalue="TRUE" falsevalue="FALSE" checked="true"
                 label="Save cluster intensity values"
                 help="Save cluster intensity for inspection."/>
      </when>

      <when value="FALSE" />

    </conditional>
  </inputs>

  <!-- =============================================================== -->
  <outputs>
    <data format="tabular" name="image_out"
          label="Processed imaging data on ${on_string}">
      <filter> process['process_selector'] == "TRUE" </filter>
    </data>
    
    <data format="rdata" name="rdata_out"
          label="R running results on ${on_string}">
          <filter> 
            ((
            process['process_selector'] == "TRUE" and
            process['rdata'] == True
            ))
          </filter>
    </data>

    <data format="pdf" name="pca_out"
          label="PCA plots on ${on_string}">
      <filter> pca['pca_selector'] == "TRUE" </filter>
    </data>

    <data format="xlsx" name="loading_out"
          label="PCA loading file on ${on_string}">
          <filter> 
            ((
            pca['pca_selector'] == "TRUE" and
            pca['loading'] == True
            ))
          </filter>
    </data>

    <data format="pdf" name="slice_out"
          label="Slice plots on ${on_string}">
      <filter> slice_selector = True </filter>
    </data>

    <data format="pdf" name="clus_out"
          label="Cluster plots on ${on_string}">
      <filter> cluster['cluster_selector'] == "TRUE" </filter>
    </data>

    <data format="tabular" name="intensity_out"
          label="Cluster intensity file on ${on_string}">
          <filter> 
            ((
            cluster['cluster_selector'] == "TRUE" and
            cluster['intensity'] == True
            ))
          </filter>
    </data>

  </outputs>

  <!-- =============================================================== -->
  <!-- 'WriteXLS' gives different size although the contents are the same -->
  <!-- different result in clustering because of randomness-->
  <tests>
    <!-- full process image -->
    <test expect_num_outputs="7">
      <expand macro="infile_imzml"/>
      <param name="process_selector" value="TRUE" /> 
      <param name="rem_outliers" value="TRUE" /> 
      <param name="summary" value="TRUE" /> 
      <param name="rdata" value="TRUE" /> 
      <param name="pca_selector" value="TRUE" /> 
      <param name="loading" value="TRUE" /> 
      <param name="slice_selector" value="TRUE" /> 
      <param name="cluster_selector" value="TRUE" /> 
      <param name="intensity" value="TRUE" /> 
      <output name="image_out" file="res/image.tsv" />
      <output name="rdata_out" file="res/r_running.rdata" compare="sim_size" />
      <output name="pca_out" file="res/pca.pdf" compare="sim_size"/>
      <!-- <output name="loading_out" file="res/loading.xlsx" compare="sim_size"/> -->
      <output name="slice_out" file="res/slice.pdf" compare="sim_size"/>
      <output name="clus_out" file="res/clus.pdf" compare="sim_size"/>
      <output name="intensity_out" file="res/intensity.tsv" />
     </test>
    <test expect_num_outputs="5">
      <expand macro="infile_imzml"/>
      <param name="process_selector" value="TRUE" /> 
      <param name="rem_outliers" value="TRUE" /> 
      <param name="summary" value="TRUE" /> 
      <param name="rdata" value="TRUE" /> 
      <param name="pca_selector" value="TRUE" /> 
      <param name="loading" value="TRUE" /> 
      <param name="slice_selector" value="TRUE" /> 
      <param name="cluster_selector" value="FALSE" /> 
      <output name="image_out" file="res/image.tsv" />
      <output name="rdata_out" file="res/r_running.rdata" compare="sim_size" />
      <output name="pca_out" file="res/pca.pdf"  compare="sim_size"/>
      <!-- <output name="loading_out" file="res/loading_1.xlsx"  compare="sim_size"/> -->
      <output name="slice_out" file="res/slice.pdf"  compare="sim_size"/>
    </test>
    <!-- pca and clustering on processed image -->
    <test expect_num_outputs="5">
      <expand macro="infile_imzml"/>
      <param name="process_selector" value="FALSE" /> 
      <param name="image_file" value="image_norm.tsv" />
      <param name="pca_selector" value="TRUE" /> 
      <param name="loading" value="TRUE" /> 
      <param name="slice_selector" value="TRUE" /> 
      <param name="cluster_selector" value="TRUE" /> 
      <param name="intensity" value="TRUE" /> 
      <!-- <output name="pca_out" file="res/pca_1.pdf"  compare="sim_size"/> -->
      <!-- <output name="loading_out" file="res/loading_1.xlsx"  compare="sim_size"/> -->
      <output name="slice_out" file="res/slice_1.pdf"  compare="sim_size"/>
      <output name="clus_out" file="res/clus_1.pdf"  compare="sim_size"/>
      <output name="intensity_out" file="res/intensity_1.tsv" />
    </test>
  </tests>

  <!-- =============================================================== -->
  <help>
massPix
=======

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

massPix_ processes high resolution mass spectrometry imaging data, performs
multivariate statistics (PCA, clustering) and lipid identification.

The overall data processing workflow consists of initial data
pre-processing, filtering, image subsetting, deisotoping, annotation,
normalisation, scaling, image "slicing" and multivariate statistics.

Data in imzML format is parsed to R. Ions with intensities greater than a
threshold, from each spectra, are extracted and grouped to user-adjustable
mass bins. Spectral features are defined by the median m/z value in each
bin, and only features detected above a threshold proportion of spectra are
retained. Average intensities for all features from a random subset of
pixels are computed and used to perform deisotoping. The deisotoping
algorithm identifies the molecular ion (M) and removes isotopes at m/z (M+1)
and (M+2) which are within a calculated proportion of the intensity of M.

Putative lipid annotation by accurate mass is achieved by searching
deisotoped ions against a generated library of lipid m/z ratios computed for
all combinations of common fatty acids, lipid head-groups and anticipated
adducts in each ionisation mode (functions: ``makelibrary`` and
``annotate``).  The criteria for a match can be adjusted according to
different MS performance capabilities. Lipid classes searched in positive
ion mode are diacylglycerides (DAG), triacylglycerides (TAG),
phosphatidylcholines (PC), phosphatidylethanolamines (PE),
phosphatidylserines (PS), LysoPC, cholesteryl esters (CE), sphingomyelins
(SM) and ceramides (Cer). In negative ion mode, lipid classes searched are
PC, phosphatidic acid (PA), PE, PS, phosphatidylglycerols (PG),
phosphatidylinositols (PI), Cer and free fatty acids (FFA). Whilst this list
is not exhaustive, it does cover the most common lipid classes. Possible
adducts considered are [M+K]+, [M+H]+, [M+Na]+, [M+NH4]+ in positive ion
mode and [M–H]-, [M+Cl]-, [M+OAc]- in negative ion mode. It is important to
point out that a database hit based on accurate mass should only be
considered the first step in metabolite identification, and confirmation
carried out using MS/MS is required, where this appropriate.

massPix_ has the further capability to perform difference matching on
deisotoped features to search for mass differences associated with
measurement-introduced alternation (e.g. loss of headgroup, loss of water)
or biological modifications (e.g. oxidation). 

The final image is constructed, based on all pixels. Ion intensities are 
then normalised either to the median or total ion count, or to the 
average intensity of a set of standard ions. 
Single ion images can be produced, or 
normalised intensities used to create multivariate statistical images 
based on k-means clustering or PCA following 
centering and Pareto scaling. 
The analysis can be readily customised by replacing default parameters 
for filtering, normalisation and scaling, library composition, lipid 
assignment and image reporting.

Inputs
------

**\1. Choose an imzml composite file**

imzml composite file actually includes two files, ``.imzml`` and ``.ibd``.
The former file contains imaging meta data while the later is the imaging
binary mass spectral data. The two files must be uploaded as an ``imzml
composite`` data type via ``Get Data``. 

**\2. Choose processed data**

If you have processed MSI data and saved the results as a tubular data
before, you can upload it for further analysis such as PCA and clustering
analysis.

Beware that you still need to load the imzml composite file even you do not
intend to process again.

Parameters
----------

The parameter setting is for processing image data and plotting. Each
section gives a brief description how to choose these parameters. 

Outputs
-------

**\1. Processed image data**

The processed image is saved in a tubular format: 

========= =================================  =======  =====================================  ================  ================
peak      annotated                          isotope  modification                           1                 2
========= =================================  =======  =====================================  ================  ================
573.4837  [DG-H20(32:0)+Na][DG-H20(34:3)+H]  [6][M]   Fragment[22] insource(phosphocholine)  568252.749061865  715704.166084769
573.4896  [DG-H20(32:0)+Na][DG-H20(34:3)+H]           Fragment[23] insource(phosphocholine)  445494.724990511  502917.999955269
573.4933  [DG-H20(34:3)+H]                                                                   96898.8800809354  259849.138593262
577.5119                                     [7][M]   Fragment[28] insource(phosphocholine)  928718.952331844  365589.233479685
577.5175  [DG-H20(34:1)+H]                   [8][M]   Fragment[29] insource(phosphocholine)  1724568.99083261  1519223.65269763
577.5236  [DG-H20(34:1)+H]                   [9][M]   Fragment[30] insource(phosphocholine)  1069278.60455705  934887.648006579
577.5277                                     [10][M]                                         147309.77849969   144416.617387283
========= =================================  =======  =====================================  ================  ================

      |

**\2. R running results** (OPTIONAL)

All running results are saved as an R file ``rdata`` for advanced user to
further analysis.

**\3. PCA plots** (OPTIONAL) 

PCA as well as its loading are plotted. Also the loading values are saved as
an Excel file. (OPTIONAL)

**\4. Slice plots** (OPTIONAL)

**\5. Cluster plots** (OPTIONAL)

Besides the cluster plots, the cluster intensity values can be saved as a
tabular format. (OPTIONAL)

  </help>
  
  <citations>
    <citation type="doi">10.1007/s11306-017-1252-5</citation>
  </citations>

</tool>