comparison dimet_metabologram.xml @ 7:06f8d9ba09cd draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 6da96d865a3a557cfa3ad09e1cfa830519e73748

6:c7ff01bd331b

            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}

    ]]></command>
    <inputs>
        <expand macro="input_parameters_metabologram"/>
        <expand macro="deg_list"/>
        <expand macro="compartments_metabologram"/>
        <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>

        <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"

            <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="statistical_test_type" value="parametric"/>
            <param name="stat_test" value="Tt"/>
            <repeat name="deg_list">
                <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="timepoint" value='T0'/>
                <repeat name="factor_list">
                    <param name="condition" value="Control"/>
                </repeat>
                <repeat name="factor_list">
                    <param name="condition" value="L-Cycloserine"/>
                </repeat>
            </repeat>
            <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[

  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**:

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.

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**

7:06f8d9ba09cd

            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: ${output_options.write_values},
            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}

    ]]></command>
    <inputs>
        <expand macro="input_parameters_metabologram"/>
        <expand macro="deg_list"/>
        <expand macro="compartments_metabologram"/>

        <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>

        <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="write_values" type="boolean" value="false" label="Write the values alongside the metabolites and genes names (e.g. L-Alanine: -0.44)"
                   help="Default value is false."/>
            <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"

            <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="statistical_test_type" value="parametric"/>
            <param name="stat_test" value="Tt"/>
            <repeat name="deg_list">
                <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="timepoint" value='T0'/>
                <repeat name="factor_list">
                    <param name="condition" value="L-Cycloserine"/>
                </repeat>
                <repeat name="factor_list">
                    <param name="condition" value="Control"/>
                </repeat>
            </repeat>
            <section name="output_options">
                <param name="show_values" value="false"/>
                <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-L-Cycloserine-T0-Control-T0--DEG_comparison1-abundances-cell.svg" name="AMINOACIDS-L-Cycloserine-T0-Control-T0--DEG_comparison1-abundances-cell" ftype="svg" compare="sim_size" delta="100"/>
                <element file="CENTRAL_CARBON_METABOLISM-L-Cycloserine-T0-Control-T0--DEG_comparison1-abundances-cell.svg" name="CENTRAL_CARBON_METABOLISM-L-Cycloserine-T0-Control-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[

  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). Please provide the file with the results of the differential expression analysis of your transcriptomics data. It is recommended to use only the statistically significant **Differentially Expressed Genes (DEG)**.  We provide examples in the zenodo (see section **Available data for testing**)



3. **The pathways files**:

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, which are of two types:

**a. Parameters proper to the metabolome differential analysis (that runs automatically before the integration)**:

- **Conditions and timepoint**:

For each comparison to run on the metabolomics data, you can define the Conditions to compare, at a chosen time point, through the box 'Deregulated gene set': follow the instructions and choose the correct order of Conditions (the last must be the reference or control).
To add a second comparison, click the 'Insert Deregulated gene set' button.
You can insert and define as many boxes ('Deregulated gene set') as comparisons you want to perform.

- **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.

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 with transcriptomics (that runs automatically after the metabolome differential analysis)**:

- **Deregulated genes set file**: Corresponds to the transcriptomics data, as explained in **Input data files** section.

For each 'Deregulated gene set' box, a single **Differentially Expressed Genes (DEG)** file must be added, and must match with the metabolomics comparison set in the same box. Additional files can be added with the 'Insert deregulated gene set' button,
see also the subsection 'Conditions and timepoint' above.

- **pathways** : files for the pathways, as explained in **Input data files** section


Overall, the metabologram module provides hints on use that will guide you, in the same menus and boxes of the parameters.


**Output**

The output consists of one figure by metabologram,  and a color key bar legend valid for all metabolograms produced

**Available data for testing**