comparison macros.xml @ 8:9c91d13827ef draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad

7:9450286c42ab

<macros>
    <token name="@TOOL_VERSION@">0.2.20</token>
    <token name="@VERSION_SUFFIX@">2</token>
    <token name="@PROFILE@">24.1</token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@TOOL_VERSION@">flexynesis</requirement>
            <yield/>

                <option value="IntegratedGradients">IntegratedGradients</option>
                <option value="GradientShap">GradientShap</option>
            </param>
        </section>
    </xml>
    <xml name="plots_common_param">
        <yield/>
        <param name="format" type="select" label="Output format">
            <option value="jpg" selected="true">jpg</option>
            <option value="png">png</option>
            <option value="pdf">pdf</option>
            <option value="svg">svg</option>
        </param>
        <param name="dpi" type="integer" min="0" max="1200" value="300" label="DPI"/>
    </xml>
    <xml name="plots_common_input">
        <yield/>
        <param argument="--labels" type="data" format="tabular" label="Predicted labels" help="Generated by flexynesis"/>

                <param name="assay" value="foo"/>
            </repeat>
            <conditional name="model_class">
                <param name="model_class" value="DirectPred"/>
            </conditional>
            <repeat name="targets">
                <param name="target_variables" value="3"/>
            </repeat>
            <param name="surv_event_var" value="15"/>
            <param name="surv_time_var" value="14"/>
            <section name="advanced">
                <param name="hpo_iter" value="1"/>
            </section>
        </conditional>
        <yield/>
        <output_collection name="results" type="list">
            <element name="job.embeddings_test">
                <assert_contents>
                    <has_n_lines n="50"/>
                </assert_contents>

            <element name="job.feature_logs.bar">
                <assert_contents>
                    <has_n_lines n="25"/>
                </assert_contents>
            </element>
            <element name="job.feature_logs.omics_foo">
                <assert_contents>
                    <has_n_lines n="25"/>
                </assert_contents>
            </element>
            <element name="job.predicted_labels">

            <element name="job.stats">
                <assert_contents>
                    <has_text_matching expression="DirectPred\tErlotinib\tnumerical\tmse\t"/>
                    <has_text_matching expression="DirectPred\tErlotinib\tnumerical\tr2\t"/>
                    <has_text_matching expression="DirectPred\tErlotinib\tnumerical\tpearson_corr\t"/>
                </assert_contents>
            </element>
        </output_collection>
    </xml>
    <token name="@COMMON_HELP@">

8:9c91d13827ef

<macros>
    <token name="@TOOL_VERSION@">0.2.20</token>
    <token name="@VERSION_SUFFIX@">3</token>
    <token name="@PROFILE@">24.1</token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@TOOL_VERSION@">flexynesis</requirement>
            <yield/>

                <option value="IntegratedGradients">IntegratedGradients</option>
                <option value="GradientShap">GradientShap</option>
            </param>
        </section>
    </xml>
    <xml name="plots_common_format">
        <param name="format" type="select" label="Output format">
            <option value="jpg" selected="true">jpg</option>
            <option value="png">png</option>
            <option value="pdf">pdf</option>
            <yield/>
        </param>
    </xml>
    <xml name="plots_common_param">
        <yield/>
        <expand macro="plots_common_format"/>
        <param name="dpi" type="integer" min="0" max="1200" value="300" label="DPI"/>
    </xml>
    <xml name="plots_common_param_svg">
        <yield/>
        <expand macro="plots_common_format">
            <option value="svg">svg</option>
        </expand>
        <param name="dpi" type="integer" min="0" max="1200" value="300" label="DPI"/>
    </xml>
    <xml name="plots_common_input">
        <yield/>
        <param argument="--labels" type="data" format="tabular" label="Predicted labels" help="Generated by flexynesis"/>

                <param name="assay" value="foo"/>
            </repeat>
            <conditional name="model_class">
                <param name="model_class" value="DirectPred"/>
            </conditional>
            <param name="target_variables" value="3"/>
            <param name="surv_event_var" value="15"/>
            <param name="surv_time_var" value="14"/>
            <section name="advanced">
                <param name="hpo_iter" value="1"/>
            </section>
            <yield/>
        </conditional>
        <output_collection name="results" type="list">
            <element name="job.embeddings_test">
                <assert_contents>
                    <has_n_lines n="50"/>
                </assert_contents>

            <element name="job.feature_logs.bar">
                <assert_contents>
                    <has_n_lines n="25"/>
                </assert_contents>
            </element>
            <element name="job.feature_logs.foo">
                <assert_contents>
                    <has_n_lines n="25"/>
                </assert_contents>
            </element>
            <element name="job.predicted_labels">

            <element name="job.stats">
                <assert_contents>
                    <has_text_matching expression="DirectPred\tErlotinib\tnumerical\tmse\t"/>
                    <has_text_matching expression="DirectPred\tErlotinib\tnumerical\tr2\t"/>
                    <has_text_matching expression="DirectPred\tErlotinib\tnumerical\tpearson_corr\t"/>
                </assert_contents>
            </element>
        </output_collection>
    </xml>
    <xml name="common_test_class">
        <param name="non_commercial_use" value="True"/>
        <conditional name="training_type">
            <param name="model" value="s_train"/>
            <param name="train_clin" value="train/clin" ftype="tabular"/>
            <param name="test_clin" value="test/clin" ftype="tabular"/>
            <param name="train_omics_main" value="train/gex" ftype="tabular"/>
            <param name="test_omics_main" value="test/gex" ftype="tabular"/>
            <param name="assay_main" value="bar"/>
            <repeat name="omics">
                <param name="train_omics" value="train/cnv" ftype="tabular"/>
                <param name="test_omics" value="test/cnv" ftype="tabular"/>
                <param name="assay" value="foo"/>
            </repeat>
            <conditional name="model_class">
                <param name="model_class" value="DirectPred"/>
            </conditional>
            <param name="target_variables" value="16"/>
            <param name="surv_event_var" value="15"/>
            <param name="surv_time_var" value="14"/>
            <section name="advanced">
                <param name="hpo_iter" value="1"/>
            </section>
            <yield/>
        </conditional>
        <output_collection name="results" type="list">
            <element name="job.embeddings_test">
                <assert_contents>
                    <has_n_lines n="50"/>
                </assert_contents>
            </element>
            <element name="job.embeddings_train">
                <assert_contents>
                    <has_n_lines n="50"/>
                </assert_contents>
            </element>
            <element name="job.feature_importance.GradientShap">
                <assert_contents>
                    <has_text_matching expression="class\t0\tbuz\tbar\tA2M\t"/>
                    <has_text_matching expression="class\t0\tbuz\tbar\tABCC4\t"/>
                    <has_text_matching expression="GradientShap"/>
                </assert_contents>
            </element>
            <element name="job.feature_importance.IntegratedGradients">
                <assert_contents>
                    <has_text_matching expression="class\t0\tbuz\tbar\tA2M\t"/>
                    <has_text_matching expression="class\t0\tbuz\tbar\tABCC4\t"/>
                    <has_text_matching expression="IntegratedGradients"/>
                </assert_contents>
            </element>
            <element name="job.feature_logs.bar">
                <assert_contents>
                    <has_n_lines n="25"/>
                </assert_contents>
            </element>
            <element name="job.feature_logs.foo">
                <assert_contents>
                    <has_n_lines n="25"/>
                </assert_contents>
            </element>
            <element name="job.predicted_labels">
                <assert_contents>
                    <has_text_matching expression="source_dataset:A-704\tclass\t"/>
                    <has_text_matching expression="target_dataset:KMRC-20\tclass\t"/>
                </assert_contents>
            </element>
            <element name="job.stats">
                <assert_contents>
                    <has_text_matching expression="DirectPred\tclass\tcategorical\tbalanced_acc\t"/>
                    <has_text_matching expression="DirectPred\tclass\tcategorical\tf1_score\t"/>
                    <has_text_matching expression="DirectPred\tclass\tcategorical\taverage_auroc\t"/>
                </assert_contents>
            </element>
        </output_collection>
    </xml>
    <token name="@COMMON_HELP@">