--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/dimet_enrichment_plot.xml	Fri Jun 21 18:45:22 2024 +0000
@@ -0,0 +1,244 @@
+<tool id="dimet_@EXECUTABLE@" name="dimet @TOOL_LABEL@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
+    <description>
+        Figures of mean enrichment by metabolite, as line-plots (by DIMet)
+    </description>
+    <macros>
+        <token name="@TOOL_LABEL@">enrichment plot</token>
+        <token name="@EXECUTABLE@">enrichment_plot</token>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
+    @INIT_CONFIG@
+    @INIT_ENRICHMENT_PLOT@
+    @INIT_PLOT_CONDITIONS@
+    @INIT_TIMEPOINTS@
+    @INIT_ENRICHMENT_METABOLITES@
+    HYDRA_FULL_ERROR=1 python -m dimet
+        '++hydra.run.dir=.'
+        '++figure_path=figures'
+        '++table_path=tables'
+        '++analysis={
+            metabolites:${metabolites},
+            dataset:{
+                _target_:dimet.data.DatasetConfig,
+                name: "Galaxy DIMet run"
+            },
+            method:{
+                _target_: dimet.method.MeanEnrichmentLinePlotConfig,
+                label: mean_enrichment_line_plot,
+                name: "Generate mean enrichment line plots",
+                palette_condition: ${output_options.palette},
+                palette_metabolite: auto_multi_color,
+                xaxis_title: ${output_options.xaxis_title},
+                alpha: ${output_options.alpha},
+                plot_grouped_by_dict: null,
+                color_lines_by: '${output_options.color_lines_by}',
+                height_subplot: ${output_options.height_subplot},
+                figure_format:${output_options.figure_format},
+                as_grid:${output_options.as_grid}
+            },
+            width_subplot: '${output_options.width_subplot}',
+            label: enrich_lineplot
+        }'
+        '++analysis.dataset.label='
+        '++analysis.timepoints=${timepoints}'
+        '++analysis.dataset.subfolder='
+        '++analysis.dataset.conditions=${conditions}'
+
+        #if $metadata_path:
+             '++analysis.dataset.metadata=metadata'
+        #end if
+        #if $me_or_frac_contrib_file:
+            '++analysis.dataset.mean_enrichment=me_or_frac_contrib'
+        #end if
+    @REMOVE_CONFIG@
+    ]]></command>
+    <inputs>
+        <expand macro="input_parameters_enrichment"/>
+        <expand macro="plot_factor_list"/>
+        <expand macro="timepoint"/>
+        <expand macro="compartments_enrichment"/>
+        <expand macro="enrichment_metabolites_list"/>
+        <section name="output_options" title="Output options">
+            <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>
+            <expand macro="palette"/>
+            <param name="color_lines_by" type="select" value="condition" display="radio" label="Select color for lines" help="Please enter at max 1 format">
+                <option value="condition">Condition</option>
+                <option value="metabolite">Metabolite</option>
+            </param>
+            <param name="alpha" type="float" min="0.0" max="1.0" value="1.0" label="alpha of subfig plots"
+                   help="Default value is 1."/>
+            <param name="height_subplot" type="float" min="1.0" max="15.0" value="6.4" label="height of subfig plots"
+                   help="Default value is 3."/>
+            <param name="width_subplot" type="float" min="1.0" max="15.0" value="4.0" label="width of subfig plots"
+                   help="Default value is 3."/>
+            <param name="as_grid" type="boolean" value="false" label="plot as grid"
+                   help="Default value is false."/>
+            <param name="xaxis_title" type="text" value="Time" optional="false" label="xaxis_title to add to output files" >
+            <sanitizer invalid_char="">
+                <valid initial="string.ascii_letters,string.digits">
+                    <add value="_" />
+                </valid>
+            </sanitizer>
+        </param>
+        </section>
+    </inputs>
+
+    <outputs>
+        <collection name="report" type="list">
+            <discover_datasets pattern="__designation_and_ext__" directory="figures"/>
+        </collection>
+    </outputs>
+    <tests>
+        <test>
+            <param name="me_or_frac_contrib_file" ftype="tabular" value="FracContribution_C.csv"/>
+            <param name="metadata_path" ftype="tabular" value="example2_metadata.csv"/>
+            <repeat name="plot_factor_list">
+                <param name="condition" value="Control"/>
+            </repeat>
+            <repeat name="plot_factor_list">
+                <param name="condition" value="L-Cycloserine"/>
+            </repeat>
+            <param name="timepoint" value='T0,T2h'/>
+            <param name="compartments" value='cell,med'/>
+            <param name="metabolites_list" value="Fumaric_acid,Glycine,L-Proline"/>
+            <section name="output_options">
+                <param name="alpha" value="1.0"/>
+                <param name="height_subplot" value="6.4"/>
+                <param name="width_subplot" value="4.0"/>
+                <param name="xaxis_title" value="Time"/>
+                <param name="color_lines_by" value="condition"/>
+                <param name="figure_format" value="svg"/>
+            </section>
+
+            <output_collection name="report" type="list" count="6">
+                <element file="mean_enrichment-cell-Fumaric_acid.svg"  name="mean_enrichment-cell-Fumaric_acid" ftype="svg" compare="sim_size" delta="100"/>
+                <element file="mean_enrichment-cell-Glycine.svg" name="mean_enrichment-cell-Glycine" ftype="svg" compare="sim_size" delta="100"/>
+                <element file="mean_enrichment-cell-L-Proline.svg" name="mean_enrichment-cell-L-Proline" ftype="svg" compare="sim_size" delta="100"/>
+                <element file="mean_enrichment-med-Fumaric_acid.svg"  name="mean_enrichment-med-Fumaric_acid" ftype="svg" compare="sim_size" delta="100"/>
+                <element file="mean_enrichment-med-Glycine.svg" name="mean_enrichment-med-Glycine" ftype="svg" compare="sim_size" delta="100"/>
+                <element file="mean_enrichment-med-L-Proline.svg" name="mean_enrichment-med-L-Proline" 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 enrichment plot performs line-plot figures for visualization of the (stable isotope) mean enrichment across all the time points present in your data, for each metabolite. 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 mean **enrichment** file, and
+
+- The metadata file, a unique file with the description of the samples. This file is compulsory (see section **Metadata File Information**).
+
+
+The mean enrichment 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 - mean **enrichment** or labeled fractional contributions:
+
+    =============== ================== ================== ================== ================== ================== ==================
+    ID              **MCF001089_TD01** **MCF001089_TD02** **MCF001089_TD03** **MCF001089_TD04** **MCF001089_TD05** **MCF001089_TD06**
+    =============== ================== ================== ================== ================== ================== ==================
+    2_3-PG          0.9711             0.968              0.9909             0.991              0.40               0.9
+    2-OHGLu         0.01719            0.0246             0.554              0.555              0.73               0.68
+    Glc6P           0.06               0.66               2683               0.06               2068               2172
+    Gly3P           0.06               0.06               0.06               1                  5                  3
+    IsoCit          0.06               1                  0.49               0.36               6                  10
+    =============== ================== ================== ================== ================== ================== ==================
+
+
+
+**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 in the legend of each figure.
+
+- **width_subplot** : the desired width (in inches) for the the individual metabolites' figures
+
+There exist hints on use that will guide you, next to the parameters.
+
+Note that this plot makes sense when you dispose of two or more time-points. If your setup is not a time-series, you may rather use our metabologram integration with the differential mean enrichment (comparing the conditions of your choice).
+
+The output consists of line-plot figures, one by each metabolite.
+
+**Available data for testing**
+
+You can test our tool with the data from our manuscript https://zenodo.org/record/10579862 (the pertinent
+files for you are located in the subfolders inside the data folder).
+You can also use the minimal data examples from https://zenodo.org/record/10579891
+
+ ]]>
+    </help>
+    <expand macro="citations"/>
+</tool>