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+<tool id="dimet_@EXECUTABLE@" name="dimet @TOOL_LABEL@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
+    <description>
+        Figures of metabolites total abundance as barplots (by DIMet)
+    </description>
+    <macros>
+        <token name="@TOOL_LABEL@">abundance plot</token>
+        <token name="@EXECUTABLE@">abundance_plot</token>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
+    @INIT_CONFIG@
+    @INIT_ABUNDANCE_PLOT@
+    @INIT_CONDITIONS@
+    @INIT_TIMEPOINTS@
+    @INIT_ENRICHMENT_METABOLITES@
+    HYDRA_FULL_ERROR=1 python -m dimet
+        -cp '$__new_file_path__/config'
+        '++hydra.run.dir=abundance_plot'
+        '++figure_path=figures'
+        '++table_path=tables'
+        '++analysis={
+            metabolites:${metabolites},
+            dataset:{
+                _target_:dimet.data.DatasetConfig,
+                name: "Galaxy DIMet run"
+            },
+            method:{
+                _target_: dimet.method.AbundancePlotConfig,
+                label: abundance_plot,
+                name: "Generate abundance plots",
+                barcolor: timepoint,
+                axisx: condition,
+                axisx_labeltilt: '${output_options.axisx_labeltilt}',
+                height_each_subfig: '${output_options.height_each_subfig}',
+                palette:${output_options.palette},
+                as_grid:${output_options.as_grid},
+                do_stripplot:${output_options.do_stripplot},
+                figure_format:${output_options.figure_format}
+            },
+            label: abundance_plot,
+            width_each_subfig: '${output_options.width_each_subfig}'
+        }'
+        '++analysis.dataset.label='
+        '++analysis.timepoints=${timepoints}'
+        '++analysis.dataset.subfolder='
+        '++analysis.dataset.conditions=${conds}'
+        #if $metadata_path:
+             '++analysis.dataset.metadata=metadata'
+        #end if
+        #if $abundance_file:
+            '++analysis.dataset.abundances=abundance'
+        #end if
+    @REMOVE_CONFIG@
+    ]]></command>
+    <inputs>
+        <expand macro="input_parameters_abundance"/>xz
+        <expand macro="conditions"/>
+        <expand macro="timepoint"/>
+        <expand macro="compartments_abundance"/>
+        <expand macro="abundance_metabolites_list"/>
+        <section name="output_options" title="Output options">
+            <param name="palette" type="select" value="pastel" display="radio" label="Select palette colormap to apply to abundance plot" help="Please enter at max 1 statistical test by file">
+                <option value="pastel">pastel</option>
+                <option value="Set1">Set1</option>
+                <option value="Set2">Set2</option>
+                <option value="Set3">Set3</option>
+                <option value="Dark2">Dark2</option>
+            </param>
+            <param name="figure_format" type="select" value="pdf" display="radio" label="Select output figure format" help="Please enter at max 1 format">
+                <option value="pdf">Pdf</option>
+                <option value="svg">Svg</option>
+            </param>
+            <param name="axisx_labeltilt" type="integer" min="0" max="180" value="70" label="X axis label tilt"
+                   help="Default value is 70."/>
+            <param name="width_each_subfig" type="float" min="1.0" max="15.0" value="3.0" label="width of subfig plots"
+                   help="Default value is 3."/>
+            <param name="height_each_subfig" type="float" min="1.0" max="15.0" value="5.5" label="height of subfig plots"
+                   help="Default value is 5.5"/>
+            <param name="as_grid" type="boolean" value="false" label="plot as grid"
+                   help="Default value is false."/>
+            <param name="do_stripplot" type="boolean" value="false" label="add strip plot on abundance bar"
+                   help="Default value is false."/>
+
+        </section>
+    </inputs>
+    <outputs>
+        <collection name="report" type="list">
+            <discover_datasets pattern="__designation_and_ext__" directory="figures"/>
+        </collection>
+    </outputs>
+    <tests>
+        <test>
+            <param name="abundance_file" ftype="tabular" value="AbundanceCorrected.csv"/>
+            <param name="metadata_path" ftype="tabular" value="example1_metadata.csv"/>
+            <param name="conditions" value='sgLDHA'/>
+            <param name="timepoint" value='T0,T24'/>
+            <param name="compartments" value='endo'/>
+            <param name="metabolites_list" value="Fru1P"/>
+            <section name="output_options">
+                <param name="axisx_labeltilt" value="70"/>
+                <param name="palette" value="pastel"/>
+                <param name="width_each_subfig" value="3.0"/>
+                <param name="height_each_subfig" value="5.5"/>
+                <param name="as_grid" value="false"/>
+                <param name="do_stripplot" value="false"/>
+                <param name="figure_format" value="svg"/>
+            </section>
+            <output_collection name="report" type="list" count="2">
+                <element file="bars_endo_Fru1P-total_abundance.svg" name="bars_endo_Fru1P-total_abundance" ftype="svg" compare="sim_size" delta="100"/>
+                <element file="legend.svg" name="legend" ftype="svg" compare="sim_size" delta="100"/>
+            </output_collection>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+This module is part of DIMet: Differential analysis of Isotope-labeled targeted Metabolomics data (https://pypi.org/project/DIMet/).
+
+DIMet total abundances plot performs comparative bars for visualization of the total abundances of each metabolite across the different conditions present in your data and all/selected time points.  All (or selected) metabolites are processed automatically.
+
+The figures in .pdf format are of publication quality, and as they are vectorial images you can open them and customize aesthetics with a professional image software such as Inkscape, Adobe Illustrator, Sketch,  CorelDRAW, etc.
+
+
+    **Input data files**
+
+For running DIMet @EXECUTABLE@ you need the following .csv files :
+
+- The total **abundances** file, and
+
+- The metadata file, a unique file with the description of the samples. This file is compulsory (see section **Metadata File Information**).
+
+
+The total abundances file must be organized as a matrix:
+- The first column must contain Metabolite IDs that are unique (not repeated) within the file.
+- The rest of the columns correspond to the samples
+- The rows correspond to the metabolites
+- The values must be tab separated, with the first row containing the sample/column labels.
+
+
+
+Example - Metabolites **abundances**:
+
+    =============== ================== ================== ================== ================== ================== ==================
+    ID              **MCF001089_TD01** **MCF001089_TD02** **MCF001089_TD03** **MCF001089_TD04** **MCF001089_TD05** **MCF001089_TD06**
+    =============== ================== ================== ================== ================== ================== ==================
+    2_3-PG          8698823.9926       10718737.7217      10724373.9         8536484.5          22060650           28898956
+    2-OHGLu         36924336           424336             92060650           45165              84951950           965165051
+    Glc6P           2310               2142               2683               1683               012532068          1252172
+    Gly3P           399298             991656565          525195             6365231            89451625           4952651963
+    IsoCit          0                  0                  0                  84915613           856236             954651610
+    =============== ================== ================== ================== ================== ================== ==================
+
+
+**Metadata File Information**
+
+Provide a tab-separated file that has the names of the samples in the first column and one header row.
+Column names must be exactly in this order:
+
+   name_to_plot
+   condition
+   timepoint
+   timenum
+   compartment
+   original_name
+
+
+Example **Metadata File**:
+
+
+    ==================== =============== ============= ============ ================ =================
+    **name_to_plot**     **condition**   **timepoint** **timenum**  **compartment**   **original_name**
+    -------------------- --------------- ------------- ------------ ---------------- -----------------
+    Control_cell_T0-1    Control         T0            0            cell             MCF001089_TD01
+    Control_cell_T0-2    Control         T0            0            cell             MCF001089_TD02
+    Control_cell_T0-3    Control         T0            0            cell             MCF001089_TD03
+    Tumoral_cell_T0-1    Tumoral         T0            0            cell             MCF001089_TD04
+    Tumoral_cell_T0-2    Tumoral         T0            0            cell             MCF001089_TD05
+    Tumoral_cell_T0-3    Tumoral         T0            0            cell             MCF001089_TD06
+    Tumoral_cell_T24-1   Tumoral         T24           24           cell             MCF001089_TD07
+    Tumoral_cell_T24-2   Tumoral         T24           24           cell             MCF001089_TD08
+    Tumoral_cell_T24-3   Tumoral         T24           24           cell             MCF001090_TD01
+    Control_med_T24-1    Control         T24           24           med              MCF001090_TD02
+    Control_med_T24-2    Control         T24           24           med              MCF001090_TD03
+    Tumoral_med_T24-1    Tumoral         T24           24           med              MCF001090_TD04
+    Tumoral_med_T24-2    Tumoral         T24           24           med              MCF001090_TD05
+    Control_med_T0-1     Control         T0            0            med              MCF001090_TD06
+    Tumoral_med_T0-1     Tumoral         T0            0            med              MCF001090_TD07
+    Tumoral_med_T0-2     Tumoral         T0            0            med              MCF001090_TD08
+    ==================== =============== ============= ============ ================ =================
+
+
+The column **original_name** must have the names of the samples as given in your data.
+
+The column **name_to_plot** must have the names as you want them to be (or set identical to original_name if you prefer). To set names that
+are meaningful is a better choice, as we will take them to display the results.
+
+The column **timenum** must contain only the numeric part of the timepoint, for example 2,0, 10, 100 (this means, without letters ("T", "t", "s", "h" etc)
+nor any other symbol). Make sure these time numbers are in the same units (but do not write the units here!).
+
+The column **compartment** is an abbreviation, coined by you, for the compartments. This will be used for the results' files names: the longer the
+compartments names are, the longer the output files' names! Please pick short and clear abbreviations to fill this column.
+
+
+**Running the analysis**
+
+
+You can precise how you want your analysis to be executed, with the parameters:
+
+- **conditions** : the conditions present in your data, exactly in the ORDER you want them to appear both in the x axis and in the legend.
+
+- **timepoints** : the selected (you can select all) time points, that will be shown in the x axis.
+
+- **width_each_subfig** : the desired width (in inches) for the the individual metabolites' figures
+
+
+
+There exist hints on use that will guide you, next to the parameters.
+
+
+The output consists of bar-plot figures, one by each metabolite, and one legend .pdf file, common to all the produced figures.
+
+
+
+**Available data for testing**
+
+You can test our tool with the data from our manuscript https://zenodo.org/record/8378887 (the pertinent
+files for you are located in the subfolders inside the data folder).
+Tou can also use the minimal data examples from https://zenodo.org/record/8380706
+
+ ]]>
+    </help>
+    <expand macro="citations"/>
+</tool>
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