changeset 0:a7d3e880e74c draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
author iuc
date Tue, 10 Oct 2023 11:56:43 +0000
parents
children 8d8ae3697a65
files dimet_metabologram.xml macros.xml test-data/AMINOACIDS-Control-T0-L-Cycloserine-T0--DEG_comparison1-abundances-cell.svg test-data/AbundanceCorrected.csv test-data/CENTRAL_CARBON_METABOLISM-Control-T0-L-Cycloserine-T0--DEG_comparison1-abundances-cell.svg test-data/CorrectedIsotopologues_reduced.csv test-data/DEG_comparison_1.csv test-data/FracContribution_C.csv test-data/Isotopologues_cell-Fructose_1,6-bisphosphate.svg test-data/Isotopologues_cell-L-Aspartic_acid.svg test-data/Isotopologues_cell-L-Glutamic_acid.svg test-data/Isotopologues_cell-L-Glutamine.svg test-data/Isotopologues_cell-L-Lactic_acid.svg test-data/Isotopologues_cell-L-Lysine.svg test-data/Isotopologues_cell-L-Proline.svg test-data/Isotopologues_cell-L-Serine.svg test-data/Isotopologues_med-L-Lactic_acid.svg test-data/Isotopologues_med-L-Lysine.svg test-data/Isotopologues_med-L-Proline.svg test-data/Isotopologues_med-L-Serine.svg test-data/abundance--cell--multigroup.tsv test-data/abundance--cell-Control-T0-L-Cycloserine-T0-Tt.tsv test-data/abundance--cell-Control-T2h-Control-T0-Tt.tsv test-data/abundance--cell-Control-T2h-L-Cycloserine-T2h-Tt.tsv test-data/abundance--cell-L-Cycloserine-T2h-L-Cycloserine-T0-Tt.tsv test-data/abundance--med-Control-T0-L-Cycloserine-T0-Tt.tsv test-data/abundance--med-Control-T2h-Control-T0-Tt.tsv test-data/abundance--med-Control-T2h-L-Cycloserine-T2h-Tt.tsv test-data/abundance--med-L-Cycloserine-T2h-L-Cycloserine-T0-Tt.tsv test-data/abundances--T0--cell--label-n_pc.svg test-data/abundances--T0--cell--label-y_pc.svg test-data/abundances--T0--cell_pc.csv test-data/abundances--T0--cell_var.csv test-data/abundances--T0--cell_var.svg test-data/abundances--T0--med--label-n_pc.svg test-data/abundances--T0--med--label-y_pc.svg test-data/abundances--T0--med_pc.csv test-data/abundances--T0--med_var.csv test-data/abundances--T0--med_var.svg test-data/abundances--T2h--cell--label-n_pc.svg test-data/abundances--T2h--cell--label-y_pc.svg test-data/abundances--T2h--cell_pc.csv test-data/abundances--T2h--cell_var.csv test-data/abundances--T2h--cell_var.svg test-data/abundances--T2h--med--label-n_pc.svg test-data/abundances--T2h--med--label-y_pc.svg test-data/abundances--T2h--med_pc.csv test-data/abundances--T2h--med_var.csv test-data/abundances--T2h--med_var.svg test-data/abundances--cell--label-n_pc.svg test-data/abundances--cell--label-y_pc.svg test-data/abundances--cell_pc.csv test-data/abundances--cell_var.csv test-data/abundances--cell_var.svg test-data/abundances--med--label-n_pc.svg test-data/abundances--med--label-y_pc.svg test-data/abundances--med_pc.csv test-data/abundances--med_var.csv test-data/abundances--med_var.svg test-data/bars_endo_Fru1P-total_abundance.svg test-data/example1_metadata.csv test-data/example2_metadata.csv test-data/example3_metadata.csv test-data/legend-abundances-cell.svg test-data/legend.svg test-data/legend_isotopologues_stackedbars.svg test-data/mean_enrichment-cell-Fumaric_acid.svg test-data/mean_enrichment-cell-Glycine.svg test-data/mean_enrichment-cell-L-Proline.svg test-data/mean_enrichment-med-Fumaric_acid.svg test-data/mean_enrichment-med-Glycine.svg test-data/mean_enrichment-med-L-Proline.svg test-data/pathways_kegg_metabolites.csv test-data/pathways_kegg_transcripts.csv test-data/rawAbundances.csv test-data/rawAbundances3.csv
diffstat 76 files changed, 48052 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/dimet_metabologram.xml	Tue Oct 10 11:56:43 2023 +0000
@@ -0,0 +1,318 @@
+<tool id="dimet_@EXECUTABLE@" name="dimet @EXECUTABLE@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
+    <description>
+        Integration of transcriptomics and (tracer) metabolomics differential data (by DIMet)
+    </description>
+    <macros>
+        <token name="@EXECUTABLE@">metabologram</token>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
+    @INIT_CONFIG@
+    @INIT_METABOLOGRAM@
+    @INIT_TRANSCRIPTS@
+    @INIT_GROUPS@
+    @INIT_COMPARISONS@
+    @INIT_PATHWAYS@
+    @INIT_STAT_TEST@
+    HYDRA_FULL_ERROR=1 python -m dimet
+    -cp '$__new_file_path__/config'
+    '++figure_path=figures'
+    '++table_path=tables'
+    '++hydra.run.dir=metabologram'
+    '++analysis={
+        dataset:{
+            _target_: dimet.data.DataIntegrationConfig,
+            name: "I am a synthetic data example"
+        },
+        method:{
+            _target_: dimet.method.MetabologramIntegrationConfig,
+            label: "metabologram",
+            name: "Perform data integration via metabologram visualization",
+            abs_values_scale_color_bar: {transcripts: null, metabolites:null},
+            colors_divergent_palette: ['royalblue', 'white', 'red'],
+            edge_color: ['black','black'],
+            line_width:['1','1.2'],
+            display_label_and_value: true,
+            font_size: ${output_options.font_size},
+            fig_width: ${output_options.fig_width},
+            figure_format:${output_options.figure_format},
+            color_nan_elements:'gray',
+            fig_height: ${output_options.fig_height}
+        },
+        columns_metabolites: {ID: metabolite, values: log2FC},
+        columns_transcripts: {ID: ${deg_one_id}, values: ${deg_one_values}},
+        compartment: cell,
+        label: metabologram
+    }'
+    '++analysis.method.qualityDistanceOverSpan='${qualityDistanceOverSpan}''
+    '++analysis.dataset.label='
+    '+analysis.timepoints=${timepoints}'
+    '++analysis.method.statistical_test=${statistical_test}'
+    '++analysis.method.grouping=${groups}'
+    '++analysis.method.correction_method=${correction_method}'
+    '++analysis.method.impute_values=${impute_values}'
+    '++analysis.statistical_test=${statistical_test}'
+    '++analysis.dataset.subfolder='
+    '++analysis.dataset.conditions=${conds}'
+    '++analysis.dataset.pathways=${pathways}'
+    '++analysis.dataset.transcripts=${transcripts}'
+    '++analysis.comparisons=${comparisons}'
+    #if $metadata_path:
+        '++analysis.dataset.metadata=metadata'
+    #end if
+    #if str( $data_input.data_input_selector ) == "abundance":
+        #if $data_input.abundance_file:
+            '++analysis.dataset.abundances=abundance'
+        #end if
+    #else:
+        #if $data_input.me_or_frac_contrib_file:
+            '++analysis.dataset.mean_enrichment=me_or_frac_contrib'
+        #end if
+    #end if
+    @REMOVE_CONFIG@
+    ]]></command>
+    <inputs>
+        <expand macro="input_parameters_metabologram"/>
+        <expand macro="deg_list"/>
+        <expand macro="conditions"/>
+        <expand macro="timepoint"/>
+        <param name="correction_method" type="select" value="bonferroni" display="radio" label="Select multiple test correction to apply" help="Please enter at max 1 method">
+                <option value="bonferroni">bonferroni</option>
+                <option value="holm-sidak">holm-sidak</option>
+                <option value="holm">holm</option>
+                <option value="simes-hochberg">simes-hochberg</option>
+                <option value="hommel">hommel</option>
+                <option value="fdr_bh">fdr_bh</option>
+                <option value="fdr_by">fdr_by</option>
+                <option value="fdr_tsbh">fdr_tsbh</option>
+                <option value="fdr_tsbky">fdr_tsbky</option>
+        </param>
+        <param name="qualityDistanceOverSpan" type="float" min="-1.0" max="-0.1" value="-0.3" label="quality Distance Over Span" help="Default value is -0.3."/>
+        <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>
+            <param name="fig_width" type="integer" min="5" max="20" value="7" label="width of figures"
+                   help="Default value is 7."/>
+            <param name="fig_height" type="integer" min="5" max="20" value="7" label="heigt of each figure"
+                   help="Default value is 7."/>
+            <param name="font_size" type="integer" min="1" max="20" value="12" label=" figure font size"
+                   help="Default value is 12."/>
+        </section>
+    </inputs>
+
+
+    <outputs>
+        <collection name="report" type="list">
+            <discover_datasets pattern="__designation_and_ext__" directory="figures"/>
+        </collection>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" ftype="tabular" value="DEG_comparison_1.csv"/>
+            <param name="idcol" ftype="integer" value="2"/>
+            <param name="valuecol" ftype="integer" value="3"/>
+            <param name="path_kegg_metabolites" ftype="tabular" value="pathways_kegg_metabolites.csv"/>
+            <param name="path_kegg_transcripts" ftype="tabular" value="pathways_kegg_transcripts.csv"/>
+            <param name="abundance_file" ftype="tabular" value="rawAbundances.csv"/>
+            <param name="metadata_path" ftype="tabular" value="example2_metadata.csv"/>
+            <param name="metabolites_list" value="Fumaric_acid,Glycine,L-Proline"/>
+            <param name="stat_test" value="Tt"/>
+            <param name="conditions" value='Control,L-Cycloserine'/>
+            <param name="timepoint" value='T0'/>
+            <section name="output_options">
+                <param name="figure_format" value="svg"/>
+                <param name="figure_width" value="7"/>
+                <param name="figure_height" value="7"/>
+                <param name="font_size" value="12"/>
+            </section>
+            <output_collection name="report" type="list" count="3">
+                <element file="AMINOACIDS-Control-T0-L-Cycloserine-T0--DEG_comparison1-abundances-cell.svg" name="AMINOACIDS-Control-T0-L-Cycloserine-T0--DEG_comparison1-abundances-cell" ftype="svg" compare="sim_size" delta="100"/>
+                <element file="CENTRAL_CARBON_METABOLISM-Control-T0-L-Cycloserine-T0--DEG_comparison1-abundances-cell.svg" name="CENTRAL_CARBON_METABOLISM-Control-T0-L-Cycloserine-T0--DEG_comparison1-abundances-cell" ftype="svg" compare="sim_size" delta="100"/>
+                <element file="legend-abundances-cell.svg" name="legend-abundances-cell" 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 Metabologram integrates tracer metabolomics and transcriptomics, in a pathway based fashion.
+More precisely, the differential information (Fold Changes (log2 transformed, or not)) of both types of omics
+must be given as input, plus the files defining the pathways. You can use the minimal data examples from https://sandbox.zenodo.org/record/1222659  that contain a minimal example data for running our DIMet Metabologram tool.
+
+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**
+
+This tool requires the following tab-delimited .csv files:
+
+1. **The metabolomics data**:
+
+  1.1 The measures' (or quantifications') files, that can be of two types:
+
+    - The total **abundances** (of the metabolites) file,
+      OR,
+
+    - The mean **enrichment** or labelled fractional contributions
+
+  1.2 The metadata, a unique file with the description of the samples in your measures' files. This is compulsory, see section **Metadata File Information**.
+
+
+2. **The transcriptomics data**:
+
+  2.1 The table with the results of the differential expression analysis (performed with an external tool)
+
+
+3. **The pathways files**:
+
+  3.1 A file with the pathways and respective gene symbols, which must match with those present in the transcriptomics data. The names of the columns must be the pathways' names, see the minimal data example downloaded from zenodo as explained above.
+
+  3.2 A file with the pathways and respective metabolites ID, that must match with those in your metabolomics data. The names of the columns must be the pathways' names, see the minimal data example downloaded from zenodo as explained above.
+
+
+
+**Measures' files**
+
+The measure's files must be organized as matrices:
+- 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.
+
+See the following examples of measures files:
+
+
+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
+    =============== ================== ================== ================== ================== ================== ==================
+
+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:
+
+
+a. Parameters proper to the metabolomics analysis (that runs automatically before the integration):
+
+- **comparisons** : the pairs of [condition, timepoint] groups to compare
+
+- **datatypes** : the measures type that you want to run, that must be only one (see above in **Input data files** section)
+
+- **statistical_test** : choose the specific statistical test to be applied.
+
+ Kruskal-Wallis, Mann-Whitney, Wilcoxon’s signed rank test, Wilcoxon’s rank sum test
+ t-test, and permutation test are currently offered (we use the trusted functions from scipy library https://docs.scipy.org/doc/scipy/reference/stats.html).
+
+For the permutation test, we have established as test statistic, the absolute difference of geometric means of the two compared groups.
+
+- **qualityDistanceOverSpan**: a normalized distance between the intervals of values of the compared groups, that is the cutoff for
+
+considering a minimal acceptable "separation", and therefore, to be suitable for statistical testing. A 'distance/span' == 1 is a perfect separation,
+whereas if 'distance/span' < 0 there is no separation.
+To use with caution in case of important dispersion of your intra-group values. Default is -0.3 (not stringent)
+
+- **correction_method** : one of the methods for multiple testing correction available in statsmodels library (bonferroni, fdr_bh, sidak, among others, see https://www.statsmodels.org/dev/generated/statsmodels.stats.multitest.multipletests.html).
+
+- **compartment** : one of the compartments present in your data.
+
+b. Parameters proper to the integration (that runs automatically after the metabolites analysis):
+
+
+- **transcripts** : the file(s) with the results of the differential expression analysis. They must be as many as the number of comparisons (metabolomics analysis) and keep a coherent order with them.
+
+- **pathways** : files for the pathways, as explained in **Input data files** section
+
+
+There exist hints on use that will guide you, next to the parameters.
+
+The output consists of one figure by metabologram,  and a color key bar legend valid for all metabolograms produced
+
+**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).
+You can also use the minimal data examples from https://zenodo.org/record/8380706
+
+ ]]>
+    </help>
+    <expand macro="citations" />
+</tool> 
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Tue Oct 10 11:56:43 2023 +0000
@@ -0,0 +1,778 @@
+<macros>
+    <token name="@TOOL_VERSION@">0.1.4</token>
+    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@EXECUTABLE@">pca</token>
+    <xml name="factor_repeat">
+        <repeat name="rep_factorName" title="Factor" min="1">
+            <param name="factorName" type="text" value="FactorName" label="Specify a factor name, e.g. effects_drug_x or cancer_markers"
+                help="Only letters, numbers and underscores will be retained in this field">
+                <sanitizer>
+                    <valid initial="string.letters,string.digits"><add value="_" /></valid>
+                </sanitizer>
+            </param>
+            <repeat name="rep_factorLevel" title="Factor level" min="2" default="2">
+                <param name="factorLevel" type="text" value="FactorLevel" label="Specify a factor level, typical values could be 'tumor', 'normal', 'treated' or 'control'"
+                    help="Only letters, numbers and underscores will be retained in this field">
+                    <sanitizer>
+                        <valid initial="string.letters,string.digits"><add value="_" /></valid>
+                    </sanitizer>
+                </param>
+                <yield/>
+            </repeat>
+        </repeat>
+    </xml>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@TOOL_VERSION@">dimet</requirement>
+        </requirements>
+    </xml>
+    <xml name="statistical_test">
+        <param name="stat_test" type="select" value="Tt"  display="radio" label="Select statistical to apply" help="Please enter at max 1 statistical test by file">
+            <option value="Tt">t-test</option>
+            <option value="MW">Mann Whitney</option>
+            <option value="KW">Kruskall Wallis</option>
+            <option value="ranksum">Wilcoxon's rank sum test</option>
+            <option value="Wcox">Wilcoxon signed-rank test</option>
+            <option value="BrMu">Brunner-Munzel test</option>
+            <option value="prm-scipy">permutations test</option>
+            <option value="disfit">distribution fitting (of the z-score of the ratios), disfit needs several hundreds of metabolites to be trustful.</option>
+        </param>
+    </xml>
+    <xml name="citations">
+        <citations>
+            <citation type="bibtex">
+                @software{Galvis_Rodriguez_DIMet,
+                    author = {Galvis Rodriguez, Johanna  and Guyon, Joris and Dartigues, Benjamin and Specque, Florian and Daubon, Thomas and Karkar, Slim and Nikolski, Macha},
+                    license = {MIT},
+                    title = {{DIMet}},
+                    url = {https://github.com/cbib/DIMet}
+                    }
+
+            </citation>
+        </citations>
+
+    </xml>
+    <xml name="metadata_file_macros">
+        <param name="metadata_path" type="data" format="tabular" label="metadata file" help="The metadata, a unique file with the description of the samples in your measures' files. This is compulsory, see section Metadata File Information."/>
+    </xml>
+    <xml name="abundance_file_macros">
+        <param name="abundance_file" type="data" format="tabular" label="Metabolite abundance file" help="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. (see help below for more details)"/>
+    </xml>
+    <xml name="enrichment_file_macros">
+        <param name="me_or_frac_contrib_file" type="data" format="tabular" label="Metabolite enrichment file" help="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. (see help below for more details)"/>
+    </xml>
+    <xml name="isotopologue_prop_file_macros">
+        <param name="isotop_prop_file" type="data" format="tabular" label="Isotopologues proportion abundance file" help="    The isotopologue proportions file must be organized as a matrix: - The first column must contain isotopologues IDs that are unique (not repeated) within the file. - The rest of the columns correspond to the samples. - The rows correspond to the isotopologues. - The values must be tab separated, with the first row containing the sample/column labels  (see help below for more details)."/>
+    </xml>
+    <xml name="isotopologue_abs_file_macros">
+        <param name="isotop_abs_file" type="data" format="tabular" label="Isotopologues absolute abundance file" help="The isotopologue absolute values file must be organized as a matrix: - The first column must contain isotopologues IDs that are unique (not repeated) within the file. - The rest of the columns correspond to the samples. - The rows correspond to the isotopologues. - The values must be tab separated, with the first row containing the sample/column labels  (see help below for more details)."/>
+    </xml>
+    <xml name="input_parameters_pca">
+        <expand macro="abundance_file_macros"/>
+        <param name="me_or_frac_contrib_file" type="data" optional="true" format="tabular" label="Mean enrichment or fraction contribution file"/>
+        <expand macro="metadata_file_macros"/>
+    </xml>
+    <xml name="input_parameters_abundance">
+        <expand macro="abundance_file_macros"/>
+        <expand macro="metadata_file_macros"/>
+    </xml>
+    <xml name="input_parameters_enrichment">
+        <expand macro="enrichment_file_macros"/>
+        <expand macro="metadata_file_macros"/>
+    </xml>
+    <xml name="input_parameters_isotopologue">
+        <expand macro="isotopologue_prop_file_macros"/>
+        <expand macro="metadata_file_macros"/>
+    </xml>
+    <xml name="input_parameters_metabologram">
+        <conditional name="data_input">
+            <param name="data_input_selector" type="select" label="Abundance, Enrichment or Isotopologues count files" help="Select between raw abundance, mean enrichment or isotopologue files">
+                <option value="abundance" selected="True">abundance</option>
+                <option value="mean_enrichment">mean_enrichment</option>
+            </param>
+            <when value="abundance">
+                <expand macro="abundance_file_macros"/>
+                <param name="metabolites_list" type="select" optional="false" multiple="true"
+                       label="Select Metabolite(s) for factor 1 to plot (1 Min.). You have to load a abundance file prior to have access to metabolite list">
+                    <validator type="length" min="1" message="Please enter at max 2 compartments"/>
+                    <options from_dataset="abundance_file">
+                        <column name="metabolite_or_isotopologue" index="0"/>
+                        <column name="value" index="0"/>
+                        <filter type="unique_value" name="metabolite_or_isotopologue" column="0"/>
+                        <filter type="remove_value" value="metabolite_or_isotopologue"/>
+                    </options>
+                    <sanitizer>
+                        <valid initial="default">
+                            <add preset="string.printable"/>
+                            <add value="\t"/>
+                            <remove value="&quot;"/>
+                            <remove value="&apos;"/>
+                        </valid>
+                    </sanitizer>
+                </param>
+                <expand macro="statistical_test"/>
+            </when>
+            <when value="mean_enrichment">
+                <expand macro="enrichment_file_macros"/>
+                <param name="metabolites_list" type="select" optional="false" multiple="true"
+                       label="Select Metabolite(s) for factor 1 to plot (1 Min.). You have to load a abundance file prior to have access to metabolite list">
+                    <validator type="length" min="1" message="Please enter at max 2 compartments"/>
+                    <options from_dataset="me_or_frac_contrib_file">
+                        <column name="metabolite_or_isotopologue" index="0"/>
+                        <column name="value" index="0"/>
+                        <filter type="unique_value" name="metabolite_or_isotopologue" column="0"/>
+                        <filter type="remove_value" value="metabolite_or_isotopologue"/>
+                    </options>
+                    <sanitizer>
+                        <valid initial="default">
+                            <add preset="string.printable"/>
+                            <add value="\t"/>
+                            <remove value="&quot;"/>
+                            <remove value="&apos;"/>
+                        </valid>
+                    </sanitizer>
+                </param>
+                <expand macro="statistical_test"/>
+            </when>
+        </conditional>
+        <param name="path_kegg_metabolites" type="data" format="tabular" label="Pathways kegg metabolites file" help="A file with the pathways and respective metabolites ID, that must match with those in your metabolomics data. The names of the columns must be the pathways' names, see the minimal data example downloaded from zenodo as explained above. (see help below for more details)"/>
+        <param name="path_kegg_transcripts" type="data" format="tabular" label="Pathways kegg transcripts file" help="A file with the pathways and respective gene symbols, which must match with those present in the transcriptomics data. The names of the columns must be the pathways' names, see the minimal data example downloaded from zenodo as explained above. (see help below for more details)"/>
+        <expand macro="metadata_file_macros"/>
+    </xml>
+    <xml name="input_parameters_diff_analysis">
+        <conditional name="data_input">
+            <param name="data_input_selector" type="select" label="Abundance, Enrichment or Isotopologues count files" help="Select between raw abundance and mean enrichment files">
+                <option value="abundance" selected="True">abundance</option>
+                <option value="mean_enrichment">mean_enrichment</option>
+                <option value="isotop_prop">isotop_prop</option>
+                <option value="isotop_abs">isotop_abs</option>
+            </param>
+            <when value="abundance">
+                <expand macro="abundance_file_macros"/>
+                <expand macro="statistical_test"/>
+
+            </when>
+            <when value="mean_enrichment">
+                <expand macro="enrichment_file_macros"/>
+                <expand macro="statistical_test"/>
+            </when>
+            <when value="isotop_prop">
+                <expand macro="isotopologue_prop_file_macros"/>
+                <expand macro="statistical_test"/>
+            </when>
+            <when value="isotop_abs">
+                <expand macro="isotopologue_abs_file_macros"/>
+                <expand macro="statistical_test"/>
+            </when>
+        </conditional>
+        <expand macro="metadata_file_macros"/>
+    </xml>
+    <xml name="suffix">
+        <param name="suffix" type="text" optional="false" label="suffix to add to output files" >
+            <sanitizer invalid_char="">
+                <valid initial="string.ascii_letters,string.digits">
+                    <add value="_" />
+                </valid>
+            </sanitizer>
+        </param>      
+    </xml>
+    <xml name="conditions">
+        <param name="conditions" type="select" optional="false" multiple="true" label="Browse conditions from metadata file (1 min. only if two timepoints are set. 2 max.). You have to load a metadata file prior to have access to metabolite list">
+            <options from_dataset="metadata_path">
+                <column name="condition" index="1"/>
+                <column name="value" index="1"/>
+                <filter type="unique_value" name="condition" column="condition"/>
+                <filter type="remove_value" value="condition"/>
+            </options>
+            <sanitizer>
+                <valid initial="default">
+                    <add preset="string.printable"/>
+                    <add value="\t"/>
+                    <remove value="&quot;"/>
+                    <remove value="&apos;"/>
+                </valid>
+            </sanitizer>
+        </param>
+    </xml>
+    <xml name="conditions_multigroup">
+        <param name="conditions" type="select" optional="false" multiple="true" label="Browse conditions from metadata file. (1 min. only if three timepoints are set). You have to load a metadata file prior to have access to conditions">
+            <options from_dataset="metadata_path">
+                <column name="condition" index="1"/>
+                <column name="value" index="1"/>
+                <filter type="unique_value" name="condition" column="condition"/>
+                <filter type="remove_value" value="condition"/>
+            </options>
+            <sanitizer>
+                <valid initial="default">
+                    <add preset="string.printable"/>
+                    <add value="\t"/>
+                    <remove value="&quot;"/>
+                    <remove value="&apos;"/>
+                </valid>
+            </sanitizer>
+        </param>
+    </xml>
+    <xml name="timepoint_multigroup">
+        <param name="timepoint" type="select" optional="true" multiple="true" label="Browse timepoint from metadata file (1 min. only if three conditions are set). You have to load a metadata file prior to have access to conditions">
+            <options from_dataset="metadata_path">
+                <column name="timepoint" index="2"/>
+                <column name="value" index="2"/>
+                <filter type="unique_value" name="timepoint" column="2"/>
+                <filter type="remove_value" value="timepoint"/>
+                <filter type="sort_by" name="timepoint" column="1"/>
+            </options>
+            <sanitizer>
+                <valid initial="default">
+                    <add preset="string.printable"/>
+                    <add value="\t"/>
+                    <remove value="&quot;"/>
+                    <remove value="&apos;"/>
+                </valid>
+            </sanitizer>
+        </param>
+    </xml>
+    <xml name="timepoint">
+        <param name="timepoint" type="select" optional="true" multiple="true" label="Browse timepoint from metadata file (1 min. only if two conditions are set.)">
+            <options from_dataset="metadata_path">
+                <column name="timepoint" index="2"/>
+                <column name="value" index="2"/>
+                <filter type="unique_value" name="timepoint" column="2"/>
+                <filter type="remove_value" value="timepoint"/>
+                <filter type="sort_by" name="timepoint" column="1"/>
+            </options>
+            <sanitizer>
+                <valid initial="default">
+                    <add preset="string.printable"/>
+                    <add value="\t"/>
+                    <remove value="&quot;"/>
+                    <remove value="&apos;"/>
+                </valid>
+            </sanitizer>
+        </param>
+    </xml>
+    <xml name="grouping">
+        <param name="grouping" type="select"  optional="false" multiple="true" label="Browse group to compare">
+            <option value="condition" selected="true">condition</option>
+            <option value="timepoint" selected="true">timepoint</option>
+        </param>
+    </xml>
+    <xml name="correction_method">
+        <param name="correction_method" type="select" value="bonferroni" display="radio" label="Select multiple test correction to apply" help="Please enter at max 1 method">
+                    <option value="bonferroni">bonferroni</option>
+                    <option value="holm-sidak">holm-sidak</option>
+                    <option value="holm">holm</option>
+                    <option value="simes-hochberg">simes-hochberg</option>
+                    <option value="hommel">hommel</option>
+                    <option value="fdr_bh">fdr_bh</option>
+                    <option value="fdr_by">fdr_by</option>
+                    <option value="fdr_tsbh">fdr_tsbh</option>
+                    <option value="fdr_tsbky">fdr_tsbky</option>
+        </param>
+    </xml>
+    <xml name="compartments_enrichment">
+        <param name="compartments" type="select" optional="false" multiple="true"
+               label="Browse compartments from metadata file (All needed). You have to load a metadata file prior to have access to compartments">
+            <options from_dataset="metadata_path">
+                <column name="compartment" index="4"/>
+                <column name="value" index="4"/>
+                <filter type="unique_value" name="compartment" column="4"/>
+                <filter type="remove_value" value="compartment"/>
+            </options>
+            <sanitizer>
+                <valid initial="default">
+                    <add preset="string.printable"/>
+                    <add value="\t"/>
+                    <remove value="&quot;"/>
+                    <remove value="&apos;"/>
+                </valid>
+            </sanitizer>
+        </param>
+    </xml>
+    <xml name="compartments_abundance">
+        <param name="compartments" type="select" optional="false" multiple="true"
+               label="Browse compartments from metadata file (All needed). You have to load a metadata file prior to have access to compartments">
+            <options from_dataset="metadata_path">
+                <column name="compartment" index="4"/>
+                <column name="value" index="4"/>
+                <filter type="unique_value" name="compartment" column="4"/>
+                <filter type="remove_value" value="compartment"/>
+            </options>
+            <sanitizer>
+                <valid initial="default">
+                    <add preset="string.printable"/>
+                    <add value="\t"/>
+                    <remove value="&quot;"/>
+                    <remove value="&apos;"/>
+                </valid>
+            </sanitizer>
+        </param>
+    </xml>
+    <xml name="compartments">
+        <param name="compartments" type="select" optional="false" multiple="true"
+               label="Browse compartments from metadata file (1 min.). You have to load a metadata file prior to have access to compartments">
+            <options from_dataset="metadata_path">
+                <column name="compartment" index="4"/>
+                <column name="value" index="4"/>
+                <filter type="unique_value" name="compartment" column="4"/>
+                <filter type="remove_value" value="compartment"/>
+            </options>
+            <sanitizer>
+                <valid initial="default">
+                    <add preset="string.printable"/>
+                    <add value="\t"/>
+                    <remove value="&quot;"/>
+                    <remove value="&apos;"/>
+                </valid>
+            </sanitizer>
+        </param>
+    </xml>
+    <xml name="abundance_metabolites_list">
+        <param name="metabolites_list" type="select" optional="false" multiple="true"
+               label="Select Metabolite(s) for factor 1 to plot (1 min). You have to load a abundance file prior to have access to metabolite list">
+            <validator type="length" min="1" message="Please enter at max 2 compartments"/>
+            <options from_dataset="abundance_file">
+                <column name="metabolite_or_isotopologue" index="0"/>
+                <column name="value" index="0"/>
+                <filter type="unique_value" name="metabolite_or_isotopologue" column="0"/>
+                <filter type="remove_value" value="metabolite_or_isotopologue"/>
+            </options>
+            <sanitizer>
+                <valid initial="default">
+                    <add preset="string.printable"/>
+                    <add value="\t"/>
+                    <remove value="&quot;"/>
+                    <remove value="&apos;"/>
+                </valid>
+            </sanitizer>
+        </param>
+    </xml>
+    <xml name="enrichment_metabolites_list">
+        <param name="metabolites_list" type="select" optional="false" multiple="true"
+               label="Select Metabolite(s) for factor 1 to plot (1 Min.). You have to load a abundance file prior to have access to metabolite list">
+            <validator type="length" min="1" message="Please enter at max 2 compartments"/>
+            <options from_dataset="me_or_frac_contrib_file">
+                <column name="ID" index="0"/>
+                <column name="value" index="0"/>
+                <filter type="unique_value" name="ID" column="0"/>
+                <filter type="remove_value" value="ID"/>
+            </options>
+            <sanitizer>
+                <valid initial="default">
+                    <add preset="string.printable"/>
+                    <add value="\t"/>
+                    <remove value="&quot;"/>
+                    <remove value="&apos;"/>
+                </valid>
+            </sanitizer>
+        </param>
+    </xml>
+    <xml name="isotopologue_metabolites_list">
+        <param name="metabolites_list" type="select" optional="false" multiple="true"
+               label="Select Metabolite(s) to plot (1 Min.). You have to load a abundance file prior to have access to metabolite list">
+            <validator type="length" min="1" message="Please enter at max 2 compartments"/>
+            <options from_dataset="isotop_prop_file">
+                <column name="ID" index="0"/>
+                <column name="value" index="0"/>
+                <filter type="unique_value" name="ID" column="0"/>
+                <filter type="remove_value" value="ID"/>
+            </options>
+            <sanitizer>
+                <valid initial="default">
+                    <add preset="string.printable"/>
+                    <add value="\t"/>
+                    <remove value="&quot;"/>
+                    <remove value="&apos;"/>
+                </valid>
+            </sanitizer>
+        </param>
+    </xml>
+    <xml name="deg_list">
+        <repeat name="deg_list" title="Deregulated gene set">
+            <param name="input" type="data" format="tabular" label="Deregulated genes set"/>
+            <param name="idcol" type="data_column" data_ref="input" label="Column for id" use_header_names="true"/>
+            <param name="valuecol" type="data_column" data_ref="input" label="Column for values" use_header_names="true"/>
+        </repeat>
+    </xml>
+    <token name="@INIT_PCA@"><![CDATA[
+    #import json
+    #import re
+
+    mkdir -p data/raw &&
+    mkdir -p data/processed &&
+
+    #if $metadata_path:
+        ln -s '$metadata_path' data/raw/metadata.csv &&
+    #end if
+    #if $abundance_file:
+        ln -s '$abundance_file' data/raw/abundance.csv &&
+    #end if
+    #if $me_or_frac_contrib_file:
+        ln -s '$me_or_frac_contrib_file' data/raw/me_or_frac_contrib.csv &&
+    #end if
+
+    ]]></token>
+    <token name="@INIT_CONFIG@"><![CDATA[
+    mkdir -p '$__new_file_path__/config' &&
+    touch '$__new_file_path__/config/config.yaml' &&
+    ]]></token>
+    <token name="@REMOVE_CONFIG@"><![CDATA[
+    && rm -r '$__new_file_path__/config'
+    ]]></token>
+    <token name="@INIT_ABUNDANCE_PLOT@"><![CDATA[
+
+    mkdir -p data/raw &&
+    mkdir -p data/processed &&
+
+    #if $metadata_path:
+        ln -s '$metadata_path' data/raw/metadata.csv &&
+    #end if
+    #if $abundance_file:
+        ln -s '$abundance_file' data/raw/abundance.csv &&
+    #end if
+    ]]></token>
+    <token name="@INIT_ENRICHMENT_PLOT@"><![CDATA[
+
+    mkdir -p data/raw &&
+    mkdir -p data/processed &&
+
+    #if $metadata_path:
+        ln -s '$metadata_path' data/raw/metadata.csv &&
+    #end if
+    #if $me_or_frac_contrib_file:
+        ln -s '$me_or_frac_contrib_file' data/raw/me_or_frac_contrib.csv &&
+    #end if
+    ]]></token>
+    <token name="@INIT_ISOTOPOLOGUE_PLOT@"><![CDATA[
+
+    mkdir -p data/raw &&
+    mkdir -p data/processed &&
+
+    #if $metadata_path:
+        ln -s '$metadata_path' data/raw/metadata.csv &&
+    #end if
+    #if $isotop_prop_file:
+        ln -s '$isotop_prop_file' data/raw/isotop_prop.csv &&
+    #end if
+    ]]></token>
+    <token name="@INIT_DIFF_ANALYSIS@"><![CDATA[
+
+    mkdir -p data/raw &&
+    mkdir -p data/processed &&
+
+    #if $metadata_path:
+        ln -s '$metadata_path' data/raw/metadata.csv &&
+    #end if
+
+    #set $impute_values  = {}
+    #if str( $data_input.data_input_selector ) == "abundance":
+        #if $data_input.abundance_file:
+            ln -s '$data_input.abundance_file' data/raw/abundance.csv &&
+            #silent $impute_values['abundances']='min'
+        #end if
+    #elif str( $data_input.data_input_selector ) == "mean_enrichment":
+        #if $data_input.me_or_frac_contrib_file:
+            ln -s '$data_input.me_or_frac_contrib_file' data/raw/me_or_frac_contrib.csv &&
+            #silent $impute_values['mean_enrichment']='min'
+        #end if
+    #elif str( $data_input.data_input_selector ) == "isotop_prop":
+        #if $data_input.isotop_prop_file:
+            ln -s '$data_input.isotop_prop_file' data/raw/isotop_prop.csv &&
+            #silent $impute_values['isotopologue_proportions']='min'
+        #end if
+    #else
+        #if $data_input.isotop_abs_file:
+            ln -s '$data_input.isotop_abs_file' data/raw/isotop_abs.csv &&
+            #silent $impute_values['isotopologues']='min'
+        #end if
+    #end if
+    ]]></token>
+    <token name="@INIT_METABOLOGRAM@"><![CDATA[
+    #import json
+    #import re
+    #import os
+    #import csv
+    #import subprocess
+
+    mkdir -p data/raw &&
+    mkdir -p data/processed &&
+    mkdir -p data/integration_files &&
+
+    #if $path_kegg_metabolites:
+        ln -s '$path_kegg_metabolites' data/integration_files/pathways_kegg_metabolites.csv &&
+    #end if
+    #if $path_kegg_transcripts:
+        ln -s '$path_kegg_transcripts' data/integration_files/pathways_kegg_transcripts.csv &&
+    #end if
+
+    #if $metadata_path:
+        ln -s '$metadata_path' data/raw/metadata.csv &&
+    #end if
+
+    #set $impute_values  = {}
+    #if str( $data_input.data_input_selector ) == "abundance":
+        #if $data_input.abundance_file:
+            ln -s '$data_input.abundance_file' data/raw/abundance.csv &&
+            #silent $impute_values['abundances']='min'
+        #end if
+    #else:
+        #if $data_input.me_or_frac_contrib_file:
+            ln -s '$data_input.me_or_frac_contrib_file' data/raw/me_or_frac_contrib.csv &&
+            #silent $impute_values['mean_enrichment']='min'
+        #end if
+    #end if
+
+    #for $i, $s in enumerate($deg_list)
+        #set $cpt = str($i+1)
+        ln -s '${s.input}' data/integration_files/DEG_comparison'${cpt}'.csv &&
+    #end for
+
+
+    ]]></token>
+    <token name="@INIT_DIFF_MULTIGROUP_ANALYSIS@"><![CDATA[
+
+    mkdir -p data/raw &&
+    mkdir -p data/processed &&
+
+    #if $metadata_path:
+        ln -s '$metadata_path' data/raw/metadata.csv &&
+    #end if
+
+    #set $impute_values  = {}
+    #if str( $data_input.data_input_selector ) == "abundance":
+        #if $data_input.abundance_file:
+            ln -s '$data_input.abundance_file' data/raw/abundance.csv &&
+            #silent $impute_values['abundances']='min'
+        #end if
+    #elif str( $data_input.data_input_selector ) == "mean_enrichment":
+        #if $data_input.me_or_frac_contrib_file:
+            ln -s '$data_input.me_or_frac_contrib_file' data/raw/me_or_frac_contrib.csv &&
+            #silent $impute_values['mean_enrichment']='min'
+        #end if
+    #elif str( $data_input.data_input_selector ) == "isotop_prop":
+        #if $data_input.isotop_prop_file:
+            ln -s '$data_input.isotop_prop_file' data/raw/isotop_prop.csv &&
+            #silent $impute_values['isotopologue_proportions']='min'
+        #end if
+    #else
+        #if $data_input.isotop_abs_file:
+            ln -s '$data_input.isotop_abs_file' data/raw/isotop_abs.csv &&
+            #silent $impute_values['isotopologues']='min'
+        #end if
+    #end if
+    ]]></token>
+    <token name="@INIT_IMPUTE_VALUES@"><![CDATA[
+    #import re
+    #set $impute_values  = {}
+    #if $abundance_file:
+        #silent $impute_values['abundances']='min'
+    #end if
+    #if $me_or_frac_contrib_file:
+        #silent $impute_values['mean_enrichment']='min'
+    #end if
+    ]]></token>
+    <token name="@INIT_DATATYPES@"><![CDATA[
+    #import re
+    #set $datatypes_avail = list()
+    #if str( $data_input.data_input_selector ) == "abundance":
+        #if $data_input.abundance_file:
+            $datatypes_avail.append(re.sub('"', '', "abundances"))
+        #end if
+    #elif str( $data_input.data_input_selector ) == "mean_enrichment":
+        #if $data_input.me_or_frac_contrib_file:
+            $datatypes_avail.append(re.sub('"', '', "mean_enrichment"))
+        #end if
+    #elif str( $data_input.data_input_selector ) == "isotop_prop":
+        #if $data_input.isotop_prop_file:
+            $datatypes_avail.append(re.sub('"', '', "isotopologue_proportions"))
+        #end if
+    #else
+        #if $data_input.isotop_abs_file:
+            $datatypes_avail.append(re.sub('"', '', "isotopologues"))
+        #end if
+    #end if
+    ]]></token>
+    <token name="@INIT_STAT_TEST@"><![CDATA[
+    #import re
+    #set $statistical_test  = {}
+    #if str( $data_input.data_input_selector ) == "abundance":
+        #if $data_input.abundance_file:
+            #silent $statistical_test['abundances']=str($data_input.stat_test)
+        #end if
+    #elif str( $data_input.data_input_selector ) == "mean_enrichment":
+        #if $data_input.me_or_frac_contrib_file:
+            #silent $statistical_test['mean_enrichment']=str($data_input.stat_test)
+        #end if
+    #elif str( $data_input.data_input_selector ) == "isotop_prop":
+        #if $data_input.isotop_prop_file:
+            #silent $statistical_test['isotopologue_proportions']=str($data_input.stat_test)
+        #end if
+    #else
+        #if $data_input.isotop_abs_file:
+            #silent $statistical_test['isotopologues']=str($data_input.stat_test)
+        #end if
+    #end if
+    ]]></token>
+    <token name="@INIT_CONDITIONS@"><![CDATA[
+    #import re
+    #set $conds = list()
+    #for $co in $conditions:
+        $conds.append(re.sub('"', '', str($co)))
+    #end for
+    ]]></token>
+    <token name="@INIT_TIMEPOINTS@"><![CDATA[
+
+    #import re
+    #set $timepoints = list()
+    #for $tp in $timepoint:
+        $timepoints.append(re.sub('"', '', str($tp)))
+    #end for
+    ]]></token>
+    <token name="@INIT_GROUPS@"><![CDATA[
+    #import re
+    #set $groups = list()
+    $groups.append(re.sub('"', '', str("condition")))
+    $groups.append(re.sub('"', '', str("timepoint")))
+
+    ]]></token>
+    <token name="@INIT_ENRICHMENT_METABOLITES@"><![CDATA[
+    #import json
+    #import re
+    #set $metabolites = {}
+    #for $cp in $compartments:
+        #silent $metabolites[re.sub('"', '', str($cp))]=list()
+        #for $met in $metabolites_list:
+            $metabolites[re.sub('"', '', str($cp))].append(re.sub('"', '\'', str($met)))
+        #end for
+    #end for
+    ]]></token>
+    <token name="@INIT_ISOTOPOLOGUE_METABOLITES@"><![CDATA[
+    #set $metabolites = {}
+    #for $cp in $compartments:
+        #silent $metabolites[re.sub('"', '', str($cp))]=list()
+        #for $met in $metabolites_list:
+            #set tmp_met=re.sub('\,', '--',str($met))
+            #set tmp_met_bis=str(re.split('_m', str($tmp_met))[0])
+            #set tmp_met_ter=re.sub('--', '\,',str($tmp_met_bis))
+            $metabolites[re.sub('"', '', str($cp))].append(re.sub('"', '\'', str(tmp_met_ter)))
+        #end for
+    #end for
+    ]]></token>
+    <token name="@INIT_MULTIGROUP_COMPARISONS@"><![CDATA[
+    #set $comparisons = list()
+    #for $tp in $timepoint:
+        #set $ctrl_found=False
+        #set $ctrl=""
+
+        #for $co in $conditions:
+            #set $sub_comparisons = list()
+            #if str($co) in ["Control", "control","ctrl"]:
+                 #set $ctrl_found=True
+                 #set $ctrl=str($co)
+                 $sub_comparisons.append(re.sub('"', '', str($co)))
+                 $sub_comparisons.append(re.sub('"', '', str($tp)))
+            #else:
+                $sub_comparisons.append(re.sub('"', '', str($co)))
+                $sub_comparisons.append(re.sub('"', '', str($tp)))
+
+            #end if
+            $comparisons.append($sub_comparisons)
+        #end for
+    #end for
+    ]]></token>
+    <token name="@INIT_CONDITIONS_TIMECOURSE@"><![CDATA[
+    #import re
+    #set $conds = list()
+    #for $co in $conditions:
+        $conds.append(re.sub('"', '', str($co)))
+    #end for
+
+    ]]></token>
+    <token name="@INIT_COMPARISONS@"><![CDATA[
+    #import re
+    #set $conds = list()
+    #for $co in $conditions:
+        $conds.append(re.sub('"', '', str($co)))
+    #end for
+    #set $timepoints = list()
+    #for $tp in $timepoint:
+        $timepoints.append(re.sub('"', '', str($tp)))
+    #end for
+
+    #set $comparisons = list()
+    #if len($conds) > 1:
+        #if len($timepoints) > 0:
+            #for $tp in $timepoint:
+                #set $ctrl_found=False
+                #set $ctrl=""
+                #set $comparisons_bis = list()
+                #for $co in $conditions:
+                    #set $sub_comparisons = list()
+                    #if str($co) in ["'Control'", "'control'", "'ctrl'"]:
+                        #set $ctrl_found=True
+                        #set $ctrl=str($co)
+                    #else:
+                        $sub_comparisons.append(re.sub('"', '', str($co)))
+                        $sub_comparisons.append(re.sub('"', '', str($tp)))
+
+                    #end if
+                    $comparisons_bis.append($sub_comparisons)
+                #end for
+
+                #if $ctrl_found:
+                    $sub_comparisons.append(str($ctrl))
+                    $sub_comparisons.append(str($tp))
+                    $comparisons_bis.append($sub_comparisons)
+                #end if
+
+                $comparisons.append($comparisons_bis)
+            #end for
+         #else
+            #for $co in $conditions:
+                $comparisons.append(re.sub('"', '', str($co)))
+            #end for
+        #end if
+
+    #else
+        #if len($conds) > 0:
+            #if len($timepoints) > 1:
+                #for $co in $conditions:
+                    #set $comparisons_bis = list()
+                    #for $tp in $timepoint:
+                        #set $sub_comparisons = list()
+                        $sub_comparisons.append(re.sub('"', '', str($co)))
+                        $sub_comparisons.append(re.sub('"', '', str($tp)))
+                        $comparisons_bis.append($sub_comparisons)
+                    #end for
+                    $comparisons.append($comparisons_bis)
+                #end for
+            #end if
+        #else
+            #for $tp in $timepoint:
+                $comparisons.append(re.sub('"', '', str($tp)))
+            #end for
+        #end if
+    #end if
+    ]]></token>
+    <token name="@INIT_TRANSCRIPTS@"><![CDATA[
+    #import re
+    #import os
+    #import subprocess
+    #set $transcripts  = list()
+
+    #for $i, $s in enumerate($deg_list)
+        #set $cpt = str($i+1)
+        $transcripts.append(re.sub('"', '', "DEG_comparison"+str($i+1)))
+        #set $deg_one_values = os.fsdecode(subprocess.check_output('head -n1 ' + str($s.input) + '| cut -f' + str($s.valuecol), shell=True))
+        #set $deg_one_id = os.fsdecode(subprocess.check_output('head -n1 ' + str($s.input) + '| cut -f' + str($s.idcol), shell=True))
+    #end for
+    ]]></token>
+    <token name="@INIT_PATHWAYS@"><![CDATA[
+    #set $pathways  = {}
+    #if $path_kegg_metabolites:
+        #silent $pathways['metabolites']='pathways_kegg_metabolites'
+    #end if
+    #if $path_kegg_transcripts:
+        #silent $pathways['transcripts']='pathways_kegg_transcripts'
+    #end if
+    ]]></token>
+</macros>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/AMINOACIDS-Control-T0-L-Cycloserine-T0--DEG_comparison1-abundances-cell.svg	Tue Oct 10 11:56:43 2023 +0000
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+++ b/test-data/CorrectedIsotopologues_reduced.csv	Tue Oct 10 11:56:43 2023 +0000
@@ -0,0 +1,46 @@
+"ID"	"MCF001089_TD01"	"MCF001089_TD02"	"MCF001089_TD07"	"MCF001089_TD08"	"MCF001089_TD19"	"MCF001089_TD20"	"MCF001089_TD25"	"MCF001089_TD26"	"MCF001089_TD37"	"MCF001089_TD38"	"MCF001089_TD43"	"MCF001089_TD44"	"MCF001089_TD55"	"MCF001089_TD56"	"MCF001089_TD61"	"MCF001089_TD62"
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/DEG_comparison_1.csv	Tue Oct 10 11:56:43 2023 +0000
@@ -0,0 +1,22 @@
+"Column_1"	"external_gene_name"	"log2FoldChange"
+"m"	"ALDOA"	4
+"n"	"GPI"	-4
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+"k"	"GLUD1"	2
+"k"	"GAD1"	-0.5
+"k"	"GLUD2"	2.7
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/FracContribution_C.csv	Tue Oct 10 11:56:43 2023 +0000
@@ -0,0 +1,26 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/abundance--cell--multigroup.tsv	Tue Oct 10 11:56:43 2023 +0000
@@ -0,0 +1,6 @@
+metabolite	Ctrl_cell_T0h-1	Ctrl_cell_T0h-2	Ctrl_cell_T0h-3	Cond1_cell_T0h-1	Cond1_cell_T0h-2	Cond1_cell_T0h-3	Cond2_cell_T0h-1	Cond2_cell_T0h-2	Cond2_cell_T0h-3	Ctrl_cell_T2h-1	Ctrl_cell_T2h-2	Ctrl_cell_T2h-3	Cond1_cell_T2h-1	Cond1_cell_T2h-2	Cond1_cell_T2h-3	Cond2_cell_T2h-1	Cond2_cell_T2h-2	Cond2_cell_T2h-3	pvalue	padj
+Glycine	0.002519	0.003212	0.002011	0.009304	0.010108	0.014663	2.87541	1.698859	1.731678	0.00015	0.000175	9.8e-05	4.5e-05	1.579707	5.3e-05	1.787379	2.109744	2.1255	0.018127	0.090635
+Hexose	0.001174	0.00082	0.001356	0.000516	0.000519	0.000437	1.843131	1.834915	2.0687	0.000169	0.000253	0.000164	1.865063	1.718398	1.76228	1.987815	2.449479	2.241466	0.006794	0.033971
+L-Arginine	0.000151	0.000198	0.000111	7.8e-05	0.00012	2.038458	2.026891	2.02749	1.983931	0.000108	0.000137	9.9e-05	2.034691	1.974143	1.917751	1.991686			0.167953	0.839766
+L-Glutamine	1.58483	1.81629	1.751614	0.754035	0.894641					3.490867	3.443824	2.831176								
+L-Tryptophan	6.3e-05	7.3e-05	7e-05	0.000491	0.000499	4.483307	0.344618	0.318892	0.313476	4e-05	4.5e-05	3.2e-05	0.369116	0.35728	0.292317	0.331011	0.300477	0.331022	0.030637	0.153184
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/abundance--cell-Control-T0-L-Cycloserine-T0-Tt.tsv	Tue Oct 10 11:56:43 2023 +0000
@@ -0,0 +1,25 @@
+metabolite	log2FC	pvalue	padj	distance/span	FC	count_nan_samples_group1	count_nan_samples_group2	distance	span_allsamples	compartment	Ctrl_cell_T0-1	Ctrl_cell_T0-2	L-Cyc_cell_T0-1	L-Cyc_cell_T0-2	gmean_1	gmean_2
+L-Tyrosine	0.659969	0.044578	1.0	0.544	1.580048	0	0	1.346502	2.475187	cell	5.059224	5.449813	3.712722	2.974626	5.250888	3.323245
+L-Methionine	0.564183	0.075348	1.0	0.488153	1.47855	0	0	1.21324	2.485367	cell	5.928871	5.711734	4.498494	3.443504	5.81929	3.935808
+L-Aspartic_acid	1.159351	0.071437	1.0	0.435311	2.23357	0	0	1.126485	2.587769	cell	3.824739	2.962785	1.8363	1.23697	3.366286	1.507132
+Ile_Leu	0.693524	0.078103	1.0	0.414254	1.617229	0	0	1.080144	2.607445	cell	4.393714	5.288745	3.31357	2.6813	4.820501	2.980717
+L-Tryptophan	0.837035	0.077877	1.0	0.411565	1.786375	0	0	1.07544	2.613053	cell	3.918551	4.59966	2.843111	1.986607	4.245468	2.376582
+L-Phenylalanine	0.676734	0.082439	1.0	0.397203	1.598517	0	0	1.043392	2.62685	cell	4.492276	5.358136	3.448884	2.731286	4.906142	3.069184
+L-Histidine	0.662413	0.124722	1.0	0.342512	1.582728	0	0	0.893231	2.607882	cell	5.135867	4.726362	3.833131	2.527985	4.926862	3.112892
+L-Lysine	0.700054	0.108484	1.0	0.32716	1.624566	0	0	0.879075	2.68699	cell	4.289814	5.133306	3.410739	2.446316	4.692646	2.888554
+L-Valine	0.48785	0.113542	1.0	0.317079	1.402354	0	0	0.853637	2.692194	cell	6.655174	5.844043	4.990406	3.96298	6.236435	4.44712
+L-Glutamic_acid	0.830004	0.137338	1.0	0.265185	1.777691	0	0	0.723262	2.727386	cell	4.556485	3.416118	2.692856	1.829099	3.945312	2.219347
+L-Serine	0.556596	0.152386	1.0	0.23191	1.470794	0	0	0.638261	2.752194	cell	5.905558	4.753595	4.115334	3.153364	5.298361	3.602381
+Hexose-phosphate	0.76747	0.157597	1.0	0.22649	1.702282	0	0	0.62225	2.747362	cell	4.735898	3.493336	2.871086	1.988536	4.067442	2.389405
+L-Proline	0.519615	0.177905	1.0	0.223644	1.433572	0	0	0.601013	2.687365	cell	6.102914	4.603201	4.002188	3.415549	5.300277	3.697252
+L-Lactic_acid	0.766316	0.216319	1.0	0.194497	1.70092	0	0	0.51042	2.624306	cell	2.828561	4.538379	2.318141	1.914073	3.582887	2.10644
+Hexose	0.648059	0.202852	1.0	0.1683	1.567058	0	0	0.459334	2.729259	cell	5.122919	3.575551	3.116217	2.39366	4.279867	2.731147
+Fumaric_acid	0.623283	0.19388	1.0	0.156841	1.540376	0	0	0.437164	2.787315	cell	3.977834	5.293909	2.506594	3.54067	4.588931	2.979098
+L-Malic_acid	0.276766	0.295582	1.0	0.151833	1.211476	0	0	0.371422	2.446251	cell	8.445961	8.514381	8.074539	6.06813	8.480102	6.999811
+L-Arginine	0.574794	0.200943	1.0	0.144438	1.489464	0	0	0.403393	2.792837	cell	4.234461	5.565819	3.831068	2.772982	4.854714	3.259368
+L-Threonine	0.540842	0.220629	1.0	0.113082	1.454821	0	0	0.316715	2.800767	cell	5.715582	4.30713	3.990415	2.914815	4.961628	3.410472
+L-Glutamine	0.98619	0.263749	1.0	0.087801	1.980946	0	0	0.237703	2.707301	cell	3.806965	2.018081	1.780378	1.099664	2.77178	1.39922
+Glycine	0.567169	0.318145	1.0	-0.012773	1.481613	0	0	-0.035287	2.762706	cell	5.028385	3.20148	3.236767	2.265679	4.012265	2.708039
+Pyruvic_acid	0.472738	0.490805	1.0	-0.131405	1.387741	0	0	-0.317152	2.413541	cell	1.811325	4.224866	2.158282	1.84113	2.766334	1.993409
+L-Alanine	0.440859	0.494601	1.0	-0.237912	1.357412	0	0	-0.631111	2.652708	cell	4.684396	2.511054	3.142165	2.031688	3.42969	2.526638
+Fructose_1,6-bisphosphate					2.638184	1	1	2.0		cell		3.220864	1.220864		3.220864	1.220864
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/abundance--cell-Control-T2h-Control-T0-Tt.tsv	Tue Oct 10 11:56:43 2023 +0000
@@ -0,0 +1,25 @@
+metabolite	log2FC	pvalue	padj	distance/span	FC	count_nan_samples_group1	count_nan_samples_group2	distance	span_allsamples	compartment	Ctrl_cell_T2h-1	Ctrl_cell_T2h-2	Ctrl_cell_T0-1	Ctrl_cell_T0-2	gmean_1	gmean_2
+L-Tryptophan	-0.777998	0.034692	0.69385	0.664552	0.583176	0	0	1.541549	2.319681	cell	2.660282	2.70099	4.242539	4.979963	2.680559	4.596486
+L-Aspartic_acid	-2.274085	0.039066	0.781312	0.556683	0.206744	0	0	1.374553	2.469185	cell	0.327076	0.791534	2.796261	2.166087	0.508814	2.461086
+L-Lysine	-0.558396	0.071556	1.0	0.497716	0.679057	0	0	1.23415	2.479625	cell	3.776027	3.993588	5.227738	6.255652	3.883284	5.718646
+L-Arginine	-0.658636	0.111701	1.0	0.440969	0.633477	0	0	1.087359	2.465839	cell	3.035924	2.953846	4.123283	5.419685	2.994604	4.72725
+L-Histidine	-0.68301	0.090057	1.0	0.413676	0.622865	0	0	1.065086	2.574685	cell	2.578187	3.676926	5.152872	4.742012	3.078929	4.943175
+L-Tyrosine	-0.589456	0.191484	1.0	0.235832	0.664593	0	0	0.617152	2.616914	cell	2.671781	4.292502	4.909654	5.288695	3.386536	5.095651
+L-Methionine	-0.489868	0.261207	1.0	0.168943	0.71209	0	0	0.427099	2.528072	cell	3.0957	4.99071	5.623772	5.417809	3.930616	5.51983
+L-Phenylalanine	-0.608451	0.19931	1.0	0.160334	0.655901	0	0	0.442554	2.760207	cell	2.526754	3.990049	4.432603	5.286961	3.175196	4.840971
+L-Malic_acid	-0.842519	0.323037	1.0	0.123892	0.557669	0	0	0.2985	2.409353	cell	1.235551	3.317115	3.615615	3.644904	2.024467	3.63023
+Ile_Leu	-0.554218	0.227774	1.0	0.111354	0.681026	0	0	0.309498	2.779406	cell	2.749607	4.283823	4.593321	5.529013	3.43203	5.039497
+L-Lactic_acid	-0.468969	0.32893	1.0	0.109159	0.722481	0	0	0.264176	2.420103	cell	3.143658	3.203459	3.467635	5.563761	3.173418	4.39239
+Fumaric_acid	-1.082458	0.257085	1.0	0.072691	0.472224	0	0	0.201376	2.770286	cell	0.878066	2.539989	2.741365	3.648352	1.493412	3.162509
+L-Glutamine	-1.091499	0.265783	1.0	0.064303	0.469274	0	0	0.177439	2.759429	cell	0.883383	1.753625	3.642812	1.931064	1.244638	2.652264
+L-Glutamic_acid	-0.765842	0.325511	1.0	-0.028187	0.58811	0	0	-0.078254	2.776208	cell	1.414087	3.21983	4.190295	3.141576	2.133804	3.628241
+L-Valine	-0.345997	0.35338	1.0	-0.044413	0.786764	0	0	-0.120212	2.706693	cell	4.179372	6.167004	6.886065	6.046792	5.07683	6.452798
+L-Threonine	-0.463814	0.368868	1.0	-0.099423	0.725067	0	0	-0.278707	2.803234	cell	2.723045	4.443183	5.526279	4.164476	3.47836	4.797297
+Pyruvic_acid	0.905946	0.398774	1.0	-0.124124	1.873772	0	0	-0.34081	2.745715	cell	1.633721	3.592255	0.84654	1.974531	2.422549	1.292873
+Hexose-phosphate	-0.60704	0.407318	1.0	-0.137592	0.656542	0	0	-0.378236	2.748963	cell	1.734049	3.685036	4.483012	3.3068	2.527851	3.85025
+Hexose	-0.403635	0.446592	1.0	-0.201612	0.755951	0	0	-0.558993	2.772623	cell	2.764282	4.423486	5.536905	3.864493	3.496822	4.625725
+L-Serine	-0.31232	0.458611	1.0	-0.2056	0.805345	0	0	-0.560471	2.726026	cell	3.868814	5.868893	6.59484	5.308422	4.765045	5.916772
+Fructose_1,6-bisphosphate				0.0	1.526778	0	1	0.0	2.23249	cell	0.154691	2.387181		0.398015	0.60768	0.398015
+Glycine	-0.316365	0.624652		-0.423447	0.803091	0	0	-1.102692	2.604084	cell	2.393939	4.284841	4.998023	3.182149	3.202756	3.988039
+L-Proline	-0.168249	0.862102		-0.454948	0.889922	0	0	-1.160081	2.549919	cell	2.590021	5.13994	4.720818	3.560737	3.648637	4.09995
+L-Alanine	-0.07162	0.950212		-0.89366	0.951569	0	0	-1.882381	2.106373	cell	1.96331	4.069683	4.057263	2.174882	2.826668	2.970533
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/abundance--cell-Control-T2h-L-Cycloserine-T2h-Tt.tsv	Tue Oct 10 11:56:43 2023 +0000
@@ -0,0 +1,25 @@
+metabolite	log2FC	pvalue	padj	distance/span	FC	count_nan_samples_group1	count_nan_samples_group2	distance	span_allsamples	compartment	Ctrl_cell_T2h-1	Ctrl_cell_T2h-2	L-Cyc_cell_T2h-1	L-Cyc_cell_T2h-2	gmean_1	gmean_2
+L-Lactic_acid	0.362066	0.35792	1.0	0.058568	1.285265	0	0	0.142099	2.42622	cell	6.256224	6.375234	3.949014	6.114125	6.315449	4.913732
+L-Arginine	0.181307	0.654333	1.0	-0.072802	1.133911	0	0	-0.192713	2.64707	cell	7.128152	6.935439	5.016926	7.663996	7.031135	6.200782
+L-Tryptophan	0.10835	0.575344	1.0	-0.075459	1.077995	0	0	-0.192682	2.553471	cell	12.591879	12.784561	10.562173	13.115644	12.687854	11.769864
+L-Lysine	0.11389	0.744288	1.0	-0.171533	1.082142	0	0	-0.462286	2.695029	cell	8.023523	8.485809	6.395727	9.090756	8.251429	7.62509
+Fumaric_acid				0.29413	0.461999	0	1	0.700935	2.383081	cell	0.888751	2.570897		3.271832	1.511584	3.271832
+Fructose_1,6-bisphosphate				0.0	1.145529	0	1	0.0	2.287469	cell	0.158501	2.44597		0.543545	0.622647	0.543545
+Pyruvic_acid	0.373873	0.661572		-0.465941	1.295827	0	0	-1.181049	2.534762	cell	1.800099	3.958089	1.423327	2.981148	2.669261	2.05989
+L-Glutamine	0.262582	0.678179		-0.482549	1.199624	0	0	-1.200459	2.487743	cell	2.308578	4.582813	2.09507	3.509037	3.252658	2.711398
+L-Aspartic_acid	0.249699	0.745614		-0.577117	1.188959	0	0	-1.388665	2.406211	cell	1.600511	3.873288	1.467077	2.989176	2.489827	2.094123
+Ile_Leu	0.191338	0.775003		-0.624008	1.141823	0	0	-1.493647	2.393636	cell	3.231426	5.034484	2.640848	4.725073	4.033431	3.53245
+L-Phenylalanine	0.185719	0.785147		-0.638734	1.137383	0	0	-1.519477	2.378888	cell	3.147058	4.969585	2.590697	4.666535	3.95469	3.477007
+L-Tyrosine	0.169586	0.805815		-0.669127	1.124736	0	0	-1.570811	2.347552	cell	3.058614	4.91399	2.566438	4.629425	3.876854	3.446902
+L-Valine	0.154185	0.813025		-0.678125	1.112793	0	0	-1.575671	2.32357	cell	3.58809	5.294519	2.970949	5.163761	4.358579	3.916793
+L-Alanine	-0.026254	0.973518		-0.688817	0.981966	0	0	-1.603905	2.328493	cell	2.170343	4.498836	2.479673	4.083578	3.124743	3.182128
+L-Histidine	0.111173	0.829889		-0.704841	1.080106	0	0	-1.624902	2.305344	cell	4.258872	6.073864	3.76852	5.883774	5.086041	4.708834
+L-Malic_acid	-0.25568	0.834034		-0.711875	0.837592	0	0	-1.640219	2.304084	cell	1.183028	3.176104	1.535885	3.487112	1.938407	2.314261
+Hexose	0.123989	0.851213		-0.738234	1.089743	0	0	-1.678448	2.273598	cell	3.154886	5.048543	2.774945	4.833334	3.990937	3.662272
+Hexose-phosphate	0.02248	0.937522		-0.772684	1.015704	0	0	-1.725995	2.233767	cell	1.985384	4.219151	2.114313	3.840308	2.894242	2.849493
+L-Glutamic_acid	0.071406	0.898587		-0.786571	1.05074	0	0	-1.739625	2.211657	cell	1.73196	3.943617	1.76515	3.504775	2.613463	2.487258
+L-Proline	-0.102609	0.921051		-0.798521	0.931347	0	0	-1.759402	2.203325	cell	2.237976	4.441301	2.617836	4.377238	3.152701	3.385098
+L-Threonine	0.069145	0.906001		-0.827452	1.049095	0	0	-1.803085	2.179081	cell	3.176783	5.183546	3.004465	4.979868	4.057955	3.868054
+L-Serine	0.075222	0.909283		-0.832574	1.053523	0	0	-1.804475	2.167344	cell	3.54649	5.379935	3.212591	5.350965	4.368053	4.146138
+L-Methionine	0.080167	0.913957		-0.840739	1.05714	0	0	-1.816896	2.16107	cell	3.053635	4.922895	2.761825	4.870531	3.877206	3.667636
+Glycine	-0.003109	0.981504		-0.842581	0.997848	0	0	-1.822182	2.162619	cell	2.737938	4.900557	2.871164	4.693346	3.66298	3.670881
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/abundance--cell-L-Cycloserine-T2h-L-Cycloserine-T0-Tt.tsv	Tue Oct 10 11:56:43 2023 +0000
@@ -0,0 +1,25 @@
+metabolite	log2FC	pvalue	padj	distance/span	FC	count_nan_samples_group1	count_nan_samples_group2	distance	span_allsamples	compartment	L-Cyc_cell_T2h-1	L-Cyc_cell_T2h-2	L-Cyc_cell_T0-1	L-Cyc_cell_T0-2	gmean_1	gmean_2
+L-Aspartic_acid	-1.364433	0.130746	0.522986	0.281466	0.388387	0	0	0.763705	2.713309	cell	0.780152	1.589563	3.493461	2.353268	1.113598	2.867237
+Pyruvic_acid	1.004811	0.273062	1.0	0.153419	2.006681	0	0	0.386767	2.520986	cell	1.764929	3.696632	1.378162	1.175646	2.55427	1.272883
+L-Proline	0.453975	0.375728	1.0	-0.027312	1.36981	0	0	-0.070115	2.567204	cell	3.208945	5.365621	3.27906	2.798417	4.149456	3.029221
+L-Alanine	0.395494	0.490938	1.0	-0.247303	1.315393	0	0	-0.66902	2.705267	cell	3.137119	5.166273	3.806139	2.461006	4.025818	3.060544
+L-Glutamine	-0.367891	0.54526		-0.322082	0.774915	0	0	-0.864197	2.683155	cell	2.384944	3.994548	5.068099	3.130351	3.086547	3.98308
+L-Arginine	-0.26515	0.569639		-0.353864	0.832112	0	0	-0.942768	2.66421	cell	3.571926	5.456573	6.236136	4.513805	4.414802	5.305535
+Ile_Leu	-0.052032	0.999845		-0.372715	0.964577	0	0	-0.987815	2.650324	cell	3.358135	6.008459	5.176894	4.189079	4.491906	4.656868
+Glycine	0.253911	0.601429		-0.381709	1.192436	0	0	-0.98425	2.578534	cell	3.495889	5.714551	4.480139	3.136017	4.469613	3.748305
+L-Tyrosine	-0.099074	0.925868		-0.397473	0.933632	0	0	-1.041848	2.621181	cell	3.260853	5.882034	5.240632	4.198784	4.379549	4.690872
+L-Valine	-0.012332	0.946093		-0.416211	0.991489	0	0	-1.085262	2.607482	cell	3.532767	6.140249	5.271324	4.186062	4.657475	4.697456
+L-Malic_acid	-0.310073	0.749772		-0.421482	0.806601	0	0	-1.063593	2.523462	cell	1.986311	4.509773	4.280295	3.216702	2.99296	3.710584
+L-Phenylalanine	-0.117435	0.894656		-0.424837	0.921825	0	0	-1.0998	2.588757	cell	3.230833	5.81959	5.2858	4.186	4.336142	4.703866
+Hexose	0.120435	0.752117		-0.433008	1.087063	0	0	-1.088815	2.51454	cell	3.389891	5.904431	4.695803	3.606988	4.473855	4.115544
+L-Lactic_acid	-0.064719	0.922245		-0.455322	0.956131	0	0	-1.16852	2.566358	cell	4.680861	7.247219	6.703809	5.535289	5.824365	6.091594
+L-Serine	0.169053	0.680458		-0.460513	1.12432	0	0	-1.121076	2.434406	cell	3.657336	6.091742	4.795994	3.674918	4.720122	4.1982
+L-Methionine	-0.005852	0.938944		-0.468109	0.995952	0	0	-1.196896	2.556876	cell	3.348806	5.905682	5.10358	3.906684	4.447132	4.465207
+Hexose-phosphate	0.13795	0.760717		-0.55418	1.10034	0	0	-1.331177	2.402066	cell	2.942487	5.344553	4.330543	2.999366	3.965637	3.604009
+L-Glutamic_acid	-0.007244	0.937477		-0.559258	0.994991	0	0	-1.377884	2.46377	cell	2.49992	4.96369	4.295701	2.917817	3.522617	3.540349
+L-Tryptophan	-0.049313	0.852261		-0.581752	0.966396	0	0	-1.40667	2.417988	cell	5.818548	7.225218	8.026356	5.608368	6.483847	6.709304
+L-Threonine	0.007882	0.940534		-0.614186	1.005478	0	0	-1.477656	2.405876	cell	3.659188	6.065064	5.482022	4.004366	4.710967	4.685299
+L-Histidine	-0.131769	0.796273		-0.655487	0.912712	0	0	-1.55048	2.365386	cell	3.449234	5.385275	5.81462	3.834795	4.309881	4.722063
+L-Lysine	0.027768	0.93853		-0.883894	1.019434	0	0	-1.871833	2.117711	cell	4.914168	6.984898	6.786001	4.867187	5.858751	5.747063
+Fructose_1,6-bisphosphate					3.516217	1	1	2.0		cell		2.794844	0.794844		2.794844	0.794844
+Fumaric_acid					1.574466	1	0	1.289051		cell		5.258464	2.81012	3.969413	5.258464	3.339839
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/abundance--med-Control-T0-L-Cycloserine-T0-Tt.tsv	Tue Oct 10 11:56:43 2023 +0000
@@ -0,0 +1,20 @@
+metabolite	log2FC	pvalue	padj	distance/span	FC	count_nan_samples_group1	count_nan_samples_group2	distance	span_allsamples	compartment	Ctrl_med_T0-1	Ctrl_med_T0-2	L-Cyc_med_T0-1	L-Cyc_med_T0-2	gmean_1	gmean_2
+L-Valine	-0.06551	0.004613	0.078425	0.830536	0.955607	0	0	1.806475	2.175072	med	42.7862	42.917067	44.961272	44.723542	42.851584	44.842249
+L-Lactic_acid	0.081287	0.035485	0.603247	0.64986	1.057961	0	0	1.519643	2.338416	med	35.285733	35.209883	33.69024	32.947317	35.247788	33.316708
+L-Arginine	0.006662	0.038909	0.661461	0.622566	1.004628	0	0	1.475052	2.369309	med	417.573697	416.802075	415.204388	415.327023	417.187708	415.265701
+L-Proline	-0.114311	0.052379	0.890451	0.495962	0.923823	0	0	1.256673	2.533809	med	22.674872	23.296347	25.208681	24.55302	22.983509	24.878691
+Hexose-phosphate	-0.152217	0.121088	1.0	0.441254	0.899867	0	0	1.07635	2.439298	med	15.686678	15.672772	18.11207	16.763028	15.679723	17.424498
+L-Tryptophan	0.139342	0.13131	1.0	0.32956	1.101403	0	0	0.861293	2.613467	med	18.793992	19.207497	17.932699	16.59403	18.99962	17.250384
+L-Phenylalanine	-0.070754	0.112054	1.0	0.327323	0.95214	0	0	0.875883	2.675902	med	34.932908	35.642687	37.60881	36.51857	35.286013	37.059681
+L-Methionine	-0.05948	0.121063	1.0	0.296729	0.95961	0	0	0.804505	2.711241	med	41.3005	42.222702	44.011741	43.027207	41.759055	43.51669
+L-Alanine	-0.186768	0.189622	1.0	0.161521	0.878572	0	0	0.450765	2.790747	med	11.17805	12.28269	13.968797	12.733455	11.71736	13.336831
+Ile_Leu	-0.067879	0.266664	1.0	0.038434	0.95404	0	0	0.108567	2.824776	med	29.783216	31.074798	32.607992	31.183365	30.422153	31.887724
+Glycine	-0.40224	0.406096	1.0	0.003298	0.756683	0	0	0.00781	2.367806	med	3.275612	3.189559	5.557365	3.283422	3.232299	4.271671
+Pyruvic_acid	-0.059155	0.334667	1.0	0.001586	0.959826	0	0	0.004213	2.65712	med	33.153112	31.141204	33.798324	33.157325	32.131415	33.47629
+L-Lysine	-0.001834	0.946483	1.0	-0.206473	0.99873	0	0	-0.57111	2.766029	med	90.619429	93.385458	92.395033	91.823923	91.992048	92.109035
+L-Threonine	-0.019183	0.467268	1.0	-0.208828	0.986792	0	0	-0.562452	2.693379	med	81.007696	78.916447	81.609826	80.445244	79.955235	81.025443
+L-Asparagine	0.051495	0.479539	1.0	-0.240516	1.036338	0	0	-0.659285	2.74113	med	30.611703	29.072045	29.73133	27.870573	29.831943	28.78592
+Hexose	0.007394	0.632326	1.0	-0.248644	1.005138	0	0	-0.634685	2.552587	med	141.526046	144.078633	142.384333	141.749648	142.796636	142.066636
+L-Serine	-0.003785	0.885659	1.0	-0.258807	0.99738	0	0	-0.70402	2.720251	med	82.756733	83.460753	84.697551	81.9773	83.107998	83.326326
+L-Histidine	0.020108	0.536681		-0.307902	1.014035	0	0	-0.82449	2.677766	med	66.478417	67.955877	65.278111	67.302907	67.213087	66.282778
+L-Tyrosine	-0.024305	0.567197		-0.345223	0.983294	0	0	-0.912759	2.643971	med	49.917227	51.3987	52.561198	50.485941	50.652548	51.51312
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/abundance--med-Control-T2h-Control-T0-Tt.tsv	Tue Oct 10 11:56:43 2023 +0000
@@ -0,0 +1,20 @@
+metabolite	log2FC	pvalue	padj	distance/span	FC	count_nan_samples_group1	count_nan_samples_group2	distance	span_allsamples	compartment	Ctrl_med_T2h-1	Ctrl_med_T2h-2	Ctrl_med_T0-1	Ctrl_med_T0-2	gmean_1	gmean_2
+L-Asparagine	-0.315743	0.028245	0.508416	0.610328	0.803437	0	0	1.473213	2.413806	med	7.730141	8.16053	10.143947	9.633743	7.942421	9.885554
+L-Phenylalanine	-0.084598	0.030111	0.541993	0.671736	0.943047	0	0	1.558881	2.320675	med	32.130034	32.052743	33.688915	34.373418	32.091365	34.029445
+L-Threonine	-0.106792	0.033603	0.604856	0.631099	0.928651	0	0	1.495659	2.369928	med	25.045012	25.211552	27.41494	26.707211	25.128144	27.058762
+L-Valine	-0.067996	0.042832	0.770972	0.607069	0.953962	0	0	1.446278	2.382394	med	39.306545	40.115539	41.561817	41.688939	39.708982	41.625329
+L-Tyrosine	-0.113457	0.046722	0.840993	0.530543	0.924371	0	0	1.321767	2.491346	med	23.066568	23.499488	24.821255	25.557914	23.282022	25.186891
+L-Serine	-0.118888	0.05061	0.910985	0.560837	0.920897	0	0	1.364531	2.433027	med	22.588437	21.723711	23.952968	24.156738	22.151855	24.054637
+Hexose-phosphate	-0.427357	0.062717	1.0	0.581387	0.743623	0	0	1.378344	2.370787	med	5.030212	6.016094	7.400999	7.394438	5.501112	7.397718
+L-Arginine	-0.065823	0.085013	1.0	0.501611	0.9554	0	0	1.222599	2.437347	med	39.86267	38.723983	41.16133	41.085269	39.289202	41.123282
+Hexose	-0.087076	0.058805	1.0	0.475511	0.941429	0	0	1.21327	2.551509	med	29.894783	30.658183	31.871453	32.446292	30.274077	32.157588
+L-Histidine	-0.096367	0.062761	1.0	0.459013	0.935385	0	0	1.179441	2.569515	med	27.526594	26.774502	28.706035	29.344017	27.147944	29.023273
+Glycine	-0.100796	0.063723	1.0	0.454918	0.932518	0	0	1.171006	2.574101	med	26.206344	25.541879	28.11598	27.37735	25.871978	27.744207
+Ile_Leu	-0.087322	0.110833	1.0	0.415844	0.941268	0	0	1.04462	2.512048	med	28.487629	28.300899	29.532249	30.812947	28.39411	30.165802
+L-Proline	-0.427205	0.130273	1.0	0.377685	0.743701	0	0	0.953724	2.525185	med	5.916471	4.533309	6.870195	7.058494	5.178918	6.963708
+L-Methionine	-0.104127	0.121198	1.0	0.325756	0.930368	0	0	0.863734	2.651476	med	22.963857	24.192125	25.055859	25.615333	23.569991	25.334052
+L-Lysine	-0.042176	0.194447	1.0	0.300247	0.971189	0	0	0.744058	2.478156	med	54.067768	54.127004	54.871062	56.545924	54.097378	55.702198
+L-Lactic_acid	-0.056578	0.275137	1.0	0.176712	0.961542	0	0	0.435423	2.464029	med	37.556173	35.609409	38.073438	37.991596	36.569839	38.032495
+L-Tryptophan	-0.176081	0.342876	1.0	0.050641	0.885104	0	0	0.126694	2.501802	med	11.638726	9.52248	11.76542	12.024282	10.527561	11.894147
+L-Alanine	-0.072231	0.842985	1.0	-0.299141	0.951166	0	0	-0.800552	2.67617	med	6.849088	9.525258	8.100928	8.90148	8.077087	8.491775
+Pyruvic_acid	0.004852	0.940585		-0.575253	1.003369	0	0	-1.407863	2.447382	med	39.928124	38.520261	40.329053	37.881671	39.217875	39.086211
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/abundance--med-Control-T2h-L-Cycloserine-T2h-Tt.tsv	Tue Oct 10 11:56:43 2023 +0000
@@ -0,0 +1,20 @@
+metabolite	log2FC	pvalue	padj	distance/span	FC	count_nan_samples_group1	count_nan_samples_group2	distance	span_allsamples	compartment	Ctrl_med_T2h-1	Ctrl_med_T2h-2	L-Cyc_med_T2h-1	L-Cyc_med_T2h-2	gmean_1	gmean_2
+L-Phenylalanine	-0.227241	0.001876	0.035636	0.905036	0.854267	0	0	1.896738	2.09576	med	11.714351	11.686171	13.781931	13.611089	11.700253	13.696244
+L-Tyrosine	-0.210967	0.004909	0.093265	0.822767	0.863958	0	0	1.796671	2.183694	med	12.524246	12.759305	14.555976	14.70794	12.641229	14.631761
+Ile_Leu	-0.219893	0.005939	0.112833	0.826897	0.858629	0	0	1.799743	2.176503	med	12.110445	12.031063	14.207566	13.910188	12.070689	14.058091
+L-Valine	-0.160198	0.012825	0.24368	0.722278	0.894902	0	0	1.65598	2.292719	med	16.643609	16.986162	18.642142	18.936328	16.814013	18.788659
+L-Threonine	-0.159992	0.019541	0.371286	0.7134	0.89503	0	0	1.632915	2.28892	med	16.648332	16.759038	18.937252	18.391953	16.703593	18.662611
+L-Proline	-0.98264	0.022874	0.434602	0.658092	0.506053	0	0	1.551275	2.35723	med	2.305637	1.766621	3.856912	4.123851	2.018214	3.988149
+Hexose	-0.2207	0.024599	0.467389	0.64383	0.858149	0	0	1.52812	2.373482	med	11.643072	11.940391	14.016554	13.468511	11.790794	13.7398
+Glycine	-0.173877	0.028221	0.536206	0.613466	0.886457	0	0	1.477944	2.409171	med	15.362891	14.973364	16.840835	17.382535	15.166877	17.109541
+L-Serine	-0.217541	0.030833	0.585825	0.595079	0.86003	0	0	1.446276	2.430393	med	12.143564	11.678687	13.58984	14.10908	11.908857	13.847026
+L-Histidine	-0.137109	0.034656	0.658468	0.574503	0.909339	0	0	1.408935	2.45244	med	19.638732	19.102155	21.047667	21.554595	19.368585	21.299623
+L-Methionine	-0.207039	0.045452	0.863579	0.525451	0.866313	0	0	1.3152	2.502993	med	12.063407	12.708642	14.023842	14.5664	12.381822	14.292547
+L-Lysine	-0.025559	0.104493	1.0	0.448561	0.98244	0	0	1.10921	2.472817	med	100.041785	100.151388	102.514602	101.260598	100.096571	101.885671
+Hexose-phosphate	-0.359685	0.092784	1.0	0.440559	0.779335	0	0	1.109796	2.519066	med	5.940748	7.105089	8.214885	8.459814	6.496887	8.33645
+L-Asparagine	-0.341921	0.124809	1.0	0.353378	0.78899	0	0	0.914077	2.586687	med	6.281405	6.631133	7.54521	8.868092	6.453901	8.179952
+L-Lactic_acid	-0.10481	0.179465	1.0	0.178872	0.929927	0	0	0.498003	2.784136	med	22.37888	21.218847	22.876883	24.002983	21.791146	23.43317
+L-Arginine	-0.030855	0.279162	1.0	0.132376	0.97884	0	0	0.337068	2.546283	med	67.988605	66.046493	68.325673	68.592776	67.010514	68.459094
+L-Alanine	-0.443451	0.222838	1.0	0.113513	0.735373	0	0	0.3169	2.79175	med	3.755311	5.222638	5.539538	6.547061	4.428615	6.022266
+Pyruvic_acid	-0.070842	0.413764	1.0	-0.116088	0.952082	0	0	-0.307971	2.652915	med	23.31152	22.489558	23.003549	25.142473	22.896851	24.049243
+L-Tryptophan	0.004678	0.946377	1.0	-0.26993	1.003247	0	0	-0.736036	2.726765	med	14.996403	12.269638	13.157757	13.893793	13.564676	13.520767
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/abundance--med-L-Cycloserine-T2h-L-Cycloserine-T0-Tt.tsv	Tue Oct 10 11:56:43 2023 +0000
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+metabolite	log2FC	pvalue	padj	distance/span	FC	count_nan_samples_group1	count_nan_samples_group2	distance	span_allsamples	compartment	L-Cyc_med_T2h-1	L-Cyc_med_T2h-2	L-Cyc_med_T0-1	L-Cyc_med_T0-2	gmean_1	gmean_2
+L-Arginine	-0.028306	0.009613	0.163421	0.808209	0.980571	0	0	1.770679	2.190869	med	99.783635	100.173715	101.944394	101.974504	99.978485	101.959448
+L-Proline	0.441124	0.016987	0.288782	0.718846	1.357661	0	0	1.64444	2.287611	med	7.203777	7.702354	5.559337	5.414743	7.448895	5.486564
+Hexose	0.141018	0.04318	0.734054	0.618875	1.102683	0	0	1.46312	2.364161	med	20.919801	20.101843	18.638723	18.55564	20.506744	18.597135
+Hexose-phosphate	-0.21989	0.073263	1.0	0.469101	0.858631	0	0	1.183673	2.523277	med	11.042011	11.371231	13.565288	12.554904	11.205412	13.050321
+L-Lactic_acid	0.129519	0.080906	1.0	0.431162	1.093929	0	0	1.107572	2.568806	med	20.843746	21.869766	19.736174	19.30096	21.350594	19.517354
+L-Phenylalanine	0.071888	0.086895	1.0	0.411507	1.051091	0	0	1.064817	2.587604	med	37.870329	37.400886	36.336069	35.282725	37.634876	35.805524
+L-Tyrosine	0.073205	0.130892	1.0	0.338927	1.052051	0	0	0.880001	2.596432	med	35.077787	35.443998	34.197786	32.847566	35.260417	33.515877
+L-Serine	0.094869	0.119025	1.0	0.303502	1.067968	0	0	0.820491	2.703409	med	27.149162	28.186476	26.328671	25.483067	27.662957	25.902419
+L-Valine	0.026692	0.156019	1.0	0.275356	1.018673	0	0	0.72888	2.647043	med	91.228609	92.66826	90.499729	90.021217	91.945617	90.260156
+L-Histidine	0.06085	0.160307	1.0	0.217054	1.04308	0	0	0.599017	2.759755	med	40.2211	41.189815	38.43006	39.622083	40.702576	39.02152
+L-Lysine	-0.018451	0.203814	1.0	0.160847	0.987293	0	0	0.441277	2.743465	med	124.61713	123.092758	125.836223	125.058407	123.852599	125.446712
+Ile_Leu	0.064692	0.208392	1.0	0.155183	1.045861	0	0	0.425368	2.741066	med	36.641515	35.874575	35.449207	33.900449	36.256017	34.66618
+L-Threonine	0.034018	0.28585	1.0	0.039028	1.02386	0	0	0.107299	2.749299	med	61.975824	60.191229	60.08393	59.226525	61.077009	59.653687
+L-Methionine	0.043433	0.307379	1.0	-0.00305	1.030563	0	0	-0.008477	2.778959	med	45.649117	47.415202	45.657594	44.636243	46.52378	45.14403
+L-Alanine	0.184452	0.318436	1.0	-0.007446	1.136385	0	0	-0.020451	2.746709	med	10.230133	12.090774	10.250584	9.344065	11.121611	9.786834
+Glycine	-0.329159	0.464864	1.0	-0.047343	0.796	0	0	-0.112992	2.386685	med	3.512786	3.625778	5.832897	3.446212	3.568835	4.483458
+Pyruvic_acid	0.016539	0.811502	1.0	-0.212837	1.01153	0	0	-0.57825	2.716869	med	29.219182	31.936051	30.489745	29.911495	30.547427	30.199236
+L-Asparagine	0.077673	0.588663		-0.337812	1.055314	0	0	-0.839365	2.484712	med	13.751007	16.161935	14.590372	13.677223	14.907813	14.126421
+L-Tryptophan	-0.041416	0.603384		-0.389154	0.971701	0	0	-1.010695	2.597159	med	26.14293	27.605347	28.740089	26.594652	26.864189	27.646567
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/abundances--T0--med_pc.csv	Tue Oct 10 11:56:43 2023 +0000
@@ -0,0 +1,5 @@
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+1.229634	-1.039134	3.021683	0.0	L-Cyc_med_T0-2	L-Cycloserine	T0	0	med	MCF001089_TD56
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/abundances--T0--med_var.csv	Tue Oct 10 11:56:43 2023 +0000
@@ -0,0 +1,5 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
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+name_to_plot	condition	timepoint	timenum	compartment	original_name
+sgLDHA_T0-1	sgLDHA	T0	0	endo	T0_A_1
+sgLDHA_T0-2	sgLDHA	T0	0	endo	T0_A_2
+sgLDHA_T24-1	sgLDHA	T24	24	endo	T24_A_1
+sgLDHA_T24-2	sgLDHA	T24	24	endo	T24_A_2
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
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+name_to_plot	condition	timepoint	timenum	compartment	original_name
+Ctrl_cell_T0-1	Control	T0	0	cell	MCF001089_TD01
+Ctrl_cell_T0-2	Control	T0	0	cell	MCF001089_TD02
+Ctrl_cell_T2h-1	Control	T2h	2	cell	MCF001089_TD07
+Ctrl_cell_T2h-2	Control	T2h	2	cell	MCF001089_TD08
+L-Cyc_cell_T0-1	L-Cycloserine	T0	0	cell	MCF001089_TD19
+L-Cyc_cell_T0-2	L-Cycloserine	T0	0	cell	MCF001089_TD20
+L-Cyc_cell_T2h-1	L-Cycloserine	T2h	2	cell	MCF001089_TD25
+L-Cyc_cell_T2h-2	L-Cycloserine	T2h	2	cell	MCF001089_TD26
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+Ctrl_med_T0-2	Control	T0	0	med	MCF001089_TD38
+Ctrl_med_T2h-1	Control	T2h	2	med	MCF001089_TD43
+Ctrl_med_T2h-2	Control	T2h	2	med	MCF001089_TD44
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+L-Cyc_med_T0-2	L-Cycloserine	T0	0	med	MCF001089_TD56
+L-Cyc_med_T2h-1	L-Cycloserine	T2h	2	med	MCF001089_TD61
+L-Cyc_med_T2h-2	L-Cycloserine	T2h	2	med	MCF001089_TD62
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
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+name_to_plot	condition	timepoint	timenum	compartment	original_name
+Ctrl_cell_T0h-1	Control	T0h	0	cell	Sample1
+Ctrl_cell_T0h-2	Control	T0h	0	cell	Sample2
+Ctrl_cell_T0h-3	Control	T0h	0	cell	Sample3
+Ctrl_cell_T2h-1	Control	T2h	2	cell	Sample4
+Ctrl_cell_T2h-2	Control	T2h	2	cell	Sample5
+Ctrl_cell_T2h-3	Control	T2h	2	cell	Sample6
+Cond1_cell_T0h-1	Cond1	T0h	0	cell	Sample7
+Cond1_cell_T0h-2	Cond1	T0h	0	cell	Sample8
+Cond1_cell_T0h-3	Cond1	T0h	0	cell	Sample9
+Cond1_cell_T2h-1	Cond1	T2h	2	cell	Sample10
+Cond1_cell_T2h-2	Cond1	T2h	2	cell	Sample11
+Cond1_cell_T2h-3	Cond1	T2h	2	cell	Sample12
+Cond2_cell_T0h-1	Cond2	T0h	0	cell	Sample13
+Cond2_cell_T0h-2	Cond2	T0h	0	cell	Sample14
+Cond2_cell_T0h-3	Cond2	T0h	0	cell	Sample15
+Cond2_cell_T2h-1	Cond2	T2h	2	cell	Sample16
+Cond2_cell_T2h-2	Cond2	T2h	2	cell	Sample17
+Cond2_cell_T2h-3	Cond2	T2h	2	cell	Sample18
\ No newline at end of file
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+++ b/test-data/pathways_kegg_metabolites.csv	Tue Oct 10 11:56:43 2023 +0000
@@ -0,0 +1,8 @@
+"CENTRAL_CARBON_METABOLISM"	"AMINOACIDS"
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+	"L-Alanine"
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/pathways_kegg_transcripts.csv	Tue Oct 10 11:56:43 2023 +0000
@@ -0,0 +1,12 @@
+"CENTRAL_CARBON_METABOLISM"	"AMINOACIDS"
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+"SUCLG1"	
+"SUCLG2"	
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rawAbundances.csv	Tue Oct 10 11:56:43 2023 +0000
@@ -0,0 +1,26 @@
+ID	MCF001089_TD01	MCF001089_TD02	MCF001089_TD07	MCF001089_TD08	MCF001089_TD19	MCF001089_TD20	MCF001089_TD25	MCF001089_TD26	MCF001089_TD37	MCF001089_TD38	MCF001089_TD43	MCF001089_TD44	MCF001089_TD55	MCF001089_TD56	MCF001089_TD61	MCF001089_TD62
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+Fumaric_acid	1765.8621555555562	2350.101706666667	565.6100944444463	1636.1451616666689	1112.7411533333332	1571.7939723809532		2082.227511666667								
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+L-Proline	6399.387268888889	4826.820016666667	3510.949071111111	6967.536411666666	4196.610013333333	3581.472580952381	4106.875117777778	6867.035166666667	6433495.033333333	6609824.833333334	5540393.533333333	4245151.533333333	7152407.533333333	6966378.033333333	9268074.033333333	9909521.833333334
+L-Serine	34591.22677111111	27843.714578333333	20292.688385555557	30783.493578333335	24105.163262666665	18470.518616190475	18382.152052222224	30617.729578333332	85713015.15666667	86442185.15666667	80830195.15666667	77735867.15666667	87723164.15666667	84905739.15666667	90456917.15666667	93913089.15666667
+L-Threonine	162184.6072	122218.556075	79915.61493	130398.02227	113231.489568	82710.40769142858	75580.73975333333	125274.2576	285717399.29	278341478.49	261018102.39	262753775.69	287841134.94	283733608.09	296904540.79	288355169.29
+L-Tryptophan	4101.068422222223	4813.902566666667	2571.5729777777774	2610.923316666667	2975.5369333333333	2079.1386666666667	2157.056777777778	2678.538611666667	23656601.733333334	24177093.733333334	23401859.733333334	19146747.733333334	22572464.733333334	20887438.733333334	20532655.733333334	21681238.733333334
+L-Tyrosine	216327.26993777775	233028.43495333332	117722.98240222223	189134.5396533333	158752.20572266664	127191.96683047619	98779.61883555555	178181.92245333333	526242843.90666664	541860987.9066666	489041215.90666664	498219681.90666664	554116402.9066666	532238404.90666664	568375310.9066666	574309133.9066666
+L-Valine	204800.46126444443	179839.41518833334	124299.92819888888	183414.65549833333	153570.35555866666	121953.23554190475	102920.69711555555	178884.87684833334	577225423.9966667	578990937.1966666	545903388.7966666	557138987.7966666	606569154.8966666	603361959.6966666	611454433.5966667	621103613.1966666
+Pyruvic_acid	629.5377555555556	1468.3793166666667	1214.9325444444444	2671.4148166666664	750.1246533333333	639.8964666666667	960.6392111111111	2012.0523166666667	1917193228.8333335	1800847679.2333333	1898133517.2333333	1831205498.1333334	1954504808.4333334	1917436849.8333335	1873057071.1333334	2047218329.5333335
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rawAbundances3.csv	Tue Oct 10 11:56:43 2023 +0000
@@ -0,0 +1,7 @@
+ID	Sample1	Sample2	Sample3	Sample4	Sample5	Sample6	Sample7	Sample8	Sample9	Sample10	Sample11	Sample12	Sample13	Sample14	Sample15	Sample16	Sample17	Sample18
+Fumaric_acid																		
+Glycine	31339.848144444444	39953.502358333335	25011.070372222222	1867.879408333334	2173.435886666666	1221.041376190477	115741.494772222224	125731.819858333336	182398.016666666	560.116666667	19650482.416666664	656.516666666	35768152.41666667	21132662.81666667	21540901.71666667	22233782.916666664	26243782.873465	26439782.65765756
+Hexose	15263.525582222223	10653.204421666667	17620.2662477777785	2194.176071666667	3284.639177333334	2131.811518095239	6702.562494444444	6744.364736666666	5678.643333334	24242428.643333334	22336054.643333334	22906432.643333334	23957348.643333334	23850557.643333334	26889340.643333334	25837975.643333334	31838775.948787	29134981.16455938
+L-Arginine	5680.366466666666	7466.331200000001	4182.386200000001	4069.3133000000003	5139.229840000001	3719.8487428571434	2943.6414666666674	4496.78815	76704557.1	76562817.1	74284491.1	72162535.1	76269336.1	76291863.1	74652772.1	74944609.1		
+L-Glutamine	8606.32958888889	9863.261441666667	9512.041427777778	18956.960391666667	18701.497033333335	15374.547080952381	4094.7460777777783	4858.299791666668										
+L-Tryptophan	4101.068422222223	4813.902566666667	4571.5729777777774	2610.923316666667	2975.5369333333333	2079.1386666666667	32157.056777777778	32678.538611666667	293656601.733333334	24177093.733333334	23401859.733333334	19146747.733333334	22572464.733333334	20887438.733333334	20532655.733333334	21681238.733333334	19681235.1976875	21681931.65426354
\ No newline at end of file