comparison dimet_enrichment_plot.xml @ 1:79720105f8c0 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 7568e92bfc4560d6e0287e7444455f55c86d135d

0:254408bfc5c0

            },
            method:{
                _target_: dimet.method.MeanEnrichmentLinePlotConfig,
                label: mean_enrichment_line_plot,
                name: "Generate mean enrichment line plots",
                color_lines_by: condition,
                palette_condition: muted,
                palette_metabolite: auto_multi_color,
                xaxis_title: ${output_options.xaxis_title},
                alpha: ${output_options.alpha},
                plot_grouped_by_dict: null,
                ###width_subplot: '${output_options.width_subplot}',
                height_subplot: ${output_options.height_subplot},
                figure_format:${output_options.figure_format},
                as_grid:${output_options.as_grid}
            },
            width_subplot: '${output_options.width_subplot}',

        <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="alpha" type="float" min="0.0" max="1.0" value="1.0" label="alpha of subfig plots"
                   help="Default value is 1."/>
            <param name="height_subplot" type="float" min="1.0" max="15.0" value="6.4" label="height of subfig plots"
                   help="Default value is 3."/>
            <param name="width_subplot" type="float" min="1.0" max="15.0" value="4.0" label="width of subfig plots"

            <section name="output_options">
                <param name="alpha" value="1.0"/>
                <param name="height_subplot" value="6.4"/>
                <param name="width_subplot" value="4.0"/>
                <param name="xaxis_title" value="Time"/>
                <param name="figure_format" value="svg"/>
            </section>

            <output_collection name="report" type="list" count="6">
                <element file="mean_enrichment-cell-Fumaric_acid.svg"  name="mean_enrichment-cell-Fumaric_acid" ftype="svg" compare="sim_size" delta="100"/>

**Available data for testing**

You can test our tool with the data from our manuscript https://zenodo.org/record/8378887 (the pertinent
files for you are located in the subfolders inside the data folder).
Tou can also use the minimal data examples from https://zenodo.org/record/8380706

 ]]>
    </help>
    <expand macro="citations"/>
</tool>

1:79720105f8c0

            },
            method:{
                _target_: dimet.method.MeanEnrichmentLinePlotConfig,
                label: mean_enrichment_line_plot,
                name: "Generate mean enrichment line plots",
                palette_condition: muted,
                palette_metabolite: auto_multi_color,
                xaxis_title: ${output_options.xaxis_title},
                alpha: ${output_options.alpha},
                plot_grouped_by_dict: null,
                color_lines_by: '${output_options.color_lines_by}',
                height_subplot: ${output_options.height_subplot},
                figure_format:${output_options.figure_format},
                as_grid:${output_options.as_grid}
            },
            width_subplot: '${output_options.width_subplot}',

        <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="color_lines_by" type="select" value="condition" display="radio" label="Select color for lines" help="Please enter at max 1 format">
                <option value="condition">Condition</option>
                <option value="metabolite">Metabolite</option>
            </param>
            <param name="alpha" type="float" min="0.0" max="1.0" value="1.0" label="alpha of subfig plots"
                   help="Default value is 1."/>
            <param name="height_subplot" type="float" min="1.0" max="15.0" value="6.4" label="height of subfig plots"
                   help="Default value is 3."/>
            <param name="width_subplot" type="float" min="1.0" max="15.0" value="4.0" label="width of subfig plots"

            <section name="output_options">
                <param name="alpha" value="1.0"/>
                <param name="height_subplot" value="6.4"/>
                <param name="width_subplot" value="4.0"/>
                <param name="xaxis_title" value="Time"/>
                <param name="color_lines_by" value="condition"/>
                <param name="figure_format" value="svg"/>
            </section>

            <output_collection name="report" type="list" count="6">
                <element file="mean_enrichment-cell-Fumaric_acid.svg"  name="mean_enrichment-cell-Fumaric_acid" ftype="svg" compare="sim_size" delta="100"/>

**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>