comparison flexynesis_plot.xml @ 2:3c5d82bf6e8a draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a

1:262c2132b392

                <option value="box_plot">Box plot</option>
            </param>
            <when value="dimred">
                <expand macro="plots_common_param">
                    <expand macro="plots_common_input"/>
                    <param argument="--embeddings" type="data" format="tabular,csv" label="Embeddings" help="Generated by flexynesis"/>
                    <param argument="--label" type="data_column" data_ref="labels" label="Column in the labels file to use for coloring the points in the plot"/>
                    <param name="method" type="select" label="Transformation method">
                        <option value="pca" selected="true">PCA</option>
                        <option value="umap">UMAP</option>
                    </param>

        <!-- test 1: dimred -->
        <test expect_num_outputs="1">
            <param name="non_commercial_use" value="True"/>
            <conditional name="plot_conditional">
                <param name="plot_type" value="dimred"/>
                <param name="embeddings" value="embeddings.csv"/>
                <param name="label" value="6"/>
                <param name="method" value="pca"/>
                <param name="labels" value="labels.csv"/>
                <param name="format" value="jpg"/>
                <param name="dpi" value="300"/>
            </conditional>
            <output name="plot_out">
                <assert_contents>

        <!-- test 2: scatter -->
        <test expect_num_outputs="1">
            <param name="non_commercial_use" value="True"/>
            <conditional name="plot_conditional">
                <param name="plot_type" value="scatter"/>
                <param name="labels" value="labels_scatter.csv"/>
                <param name="true_label" value="5"/>
                <param name="predicted_label" value="6"/>
                <param name="format" value="jpg"/>
                <param name="dpi" value="300"/>
            </conditional>

        <!-- test 3: concordance_heatmap -->
        <test expect_num_outputs="1">
            <param name="non_commercial_use" value="True"/>
            <conditional name="plot_conditional">
                <param name="plot_type" value="concordance_heatmap"/>
                <param name="labels" value="labels.csv"/>
                <param name="true_label" value="5"/>
                <param name="predicted_label" value="6"/>
                <param name="format" value="jpg"/>
                <param name="dpi" value="300"/>
            </conditional>

        <!-- test 4: pr_curve -->
        <test expect_num_outputs="1">
            <param name="non_commercial_use" value="True"/>
            <conditional name="plot_conditional">
                <param name="plot_type" value="pr_curve"/>
                <param name="labels" value="labels_pr.csv"/>
                <param name="format" value="jpg"/>
                <param name="dpi" value="300"/>
            </conditional>
            <output name="plot_out">
                <assert_contents>

        <!-- test 5: roc_curve -->
        <test expect_num_outputs="1">
            <param name="non_commercial_use" value="True"/>
            <conditional name="plot_conditional">
                <param name="plot_type" value="roc_curve"/>
                <param name="labels" value="labels_pr.csv"/>
                <param name="format" value="jpg"/>
                <param name="dpi" value="300"/>
            </conditional>
            <output name="plot_out">
                <assert_contents>

        <!-- test 6: box_plot -->
        <test expect_num_outputs="1">
            <param name="non_commercial_use" value="True"/>
            <conditional name="plot_conditional">
                <param name="plot_type" value="box_plot"/>
                <param name="labels" value="labels_pr.csv"/>
                <param name="format" value="jpg"/>
                <param name="dpi" value="300"/>
            </conditional>
            <output_collection name="boxplot_out" type="list" count="7">
                <element name="box_plot_Basal">

2:3c5d82bf6e8a

                <option value="box_plot">Box plot</option>
            </param>
            <when value="dimred">
                <expand macro="plots_common_param">
                    <expand macro="plots_common_input"/>
                    <param argument="--embeddings" type="data" format="tabular" label="Embeddings" help="Generated by flexynesis"/>
                    <param argument="--label" type="data_column" data_ref="labels" label="Column in the labels file to use for coloring the points in the plot"/>
                    <param name="method" type="select" label="Transformation method">
                        <option value="pca" selected="true">PCA</option>
                        <option value="umap">UMAP</option>
                    </param>

        <!-- test 1: dimred -->
        <test expect_num_outputs="1">
            <param name="non_commercial_use" value="True"/>
            <conditional name="plot_conditional">
                <param name="plot_type" value="dimred"/>
                <param name="embeddings" value="embeddings.tabular"/>
                <param name="label" value="6"/>
                <param name="method" value="pca"/>
                <param name="labels" value="labels.tabular"/>
                <param name="format" value="jpg"/>
                <param name="dpi" value="300"/>
            </conditional>
            <output name="plot_out">
                <assert_contents>

        <!-- test 2: scatter -->
        <test expect_num_outputs="1">
            <param name="non_commercial_use" value="True"/>
            <conditional name="plot_conditional">
                <param name="plot_type" value="scatter"/>
                <param name="labels" value="labels_scatter.tabular"/>
                <param name="true_label" value="5"/>
                <param name="predicted_label" value="6"/>
                <param name="format" value="jpg"/>
                <param name="dpi" value="300"/>
            </conditional>

        <!-- test 3: concordance_heatmap -->
        <test expect_num_outputs="1">
            <param name="non_commercial_use" value="True"/>
            <conditional name="plot_conditional">
                <param name="plot_type" value="concordance_heatmap"/>
                <param name="labels" value="labels.tabular"/>
                <param name="true_label" value="5"/>
                <param name="predicted_label" value="6"/>
                <param name="format" value="jpg"/>
                <param name="dpi" value="300"/>
            </conditional>

        <!-- test 4: pr_curve -->
        <test expect_num_outputs="1">
            <param name="non_commercial_use" value="True"/>
            <conditional name="plot_conditional">
                <param name="plot_type" value="pr_curve"/>
                <param name="labels" value="labels_pr.tabular"/>
                <param name="format" value="jpg"/>
                <param name="dpi" value="300"/>
            </conditional>
            <output name="plot_out">
                <assert_contents>

        <!-- test 5: roc_curve -->
        <test expect_num_outputs="1">
            <param name="non_commercial_use" value="True"/>
            <conditional name="plot_conditional">
                <param name="plot_type" value="roc_curve"/>
                <param name="labels" value="labels_pr.tabular"/>
                <param name="format" value="jpg"/>
                <param name="dpi" value="300"/>
            </conditional>
            <output name="plot_out">
                <assert_contents>

        <!-- test 6: box_plot -->
        <test expect_num_outputs="1">
            <param name="non_commercial_use" value="True"/>
            <conditional name="plot_conditional">
                <param name="plot_type" value="box_plot"/>
                <param name="labels" value="labels_pr.tabular"/>
                <param name="format" value="jpg"/>
                <param name="dpi" value="300"/>
            </conditional>
            <output_collection name="boxplot_out" type="list" count="7">
                <element name="box_plot_Basal">