comparison macros.xml @ 4:07f018886d40 draft

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

3:e6b783c597b3

<macros>
    <token name="@TOOL_VERSION@">0.2.20</token>
    <token name="@VERSION_SUFFIX@">1</token>
    <token name="@PROFILE@">24.1</token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@TOOL_VERSION@">flexynesis</requirement>
            <yield/>

        <param name="non_commercial_use" label="I certify that I am not using this tool for commercial purposes." type="boolean" truevalue="NON_COMMERCIAL_USE" falsevalue="COMMERCIAL_USE" checked="False">
            <validator type="expression" message="This tool is only available for non-commercial use.">value == True</validator>
        </param>
    </xml>
    <xml name="main_inputs">
        <param name="train_clin" type="data" format="csv" label="Training clinical data"/>
        <param name="test_clin" type="data" format="csv" label="Test clinical data"/>
        <param name="train_omics_main" type="data" format="csv" label="Training omics data"/>
        <param name="test_omics_main" type="data" format="csv" label="Test omics data"/>
        <param name="assay_main" type="text" optional="true" label="What type of assay is your input?" help="This would be used as output name.">
            <expand macro="sanitizer_letters"/>
        </param>
    </xml>
    <xml name="extra_inputs">
        <param name="train_omics" type="data" optional="true" format="csv" label="Training omics data"/>
        <param name="test_omics" type="data" optional="true" format="csv" label="Test omics data"/>
        <param name="assay" type="text" optional="true" label="What type of assay is your input?" help="This would be used as output name." >
            <expand macro="sanitizer_letters"/>
        </param>
    </xml>
    <xml name="advanced">

        </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,csv" label="Predicted labels" help="Generated by flexynesis"/>
    </xml>
    <token name="@PLOT_COMMON_CONFIG@"><![CDATA[
label_data = load_labels('inputs/$plot_conditional.labels.element_identifier.$plot_conditional.labels.ext')
    ]]></token>
    <token name="@PR_ROC_BOX_CONFIG@"><![CDATA[

    ]]></token>
    <xml name="common_test">
        <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="csv"/>
            <param name="test_clin" value="test/clin" ftype="csv"/>
            <param name="train_omics_main" value="train/gex" ftype="csv"/>
            <param name="test_omics_main" value="test/gex" ftype="csv"/>
            <param name="assay_main" value="bar"/>
            <repeat name="omics">
                <param name="train_omics" value="train/cnv" ftype="csv"/>
                <param name="test_omics" value="test/cnv" ftype="csv"/>
                <param name="assay" value="foo"/>
            </repeat>
            <conditional name="model_class">
                <param name="model_class" value="DirectPred"/>
            </conditional>
            <param name="target_variables" value="Erlotinib"/>
            <param name="surv_event_var" value="OS_STATUS"/>
            <param name="surv_time_var" value="OS_MONTHS"/>
            <section name="advanced">
                <param name="hpo_iter" value="1"/>
            </section>
        </conditional>
        <yield/>

                    <has_n_lines n="50"/>
                </assert_contents>
            </element>
            <element name="job.feature_importance.GradientShap">
                <assert_contents>
                    <has_text_matching expression="Erlotinib,0,,bar,A2M,"/>
                    <has_text_matching expression="Erlotinib,0,,bar,ABCC4,"/>
                    <has_text_matching expression="GradientShap"/>
                </assert_contents>
            </element>
            <element name="job.feature_importance.IntegratedGradients">
                <assert_contents>
                    <has_text_matching expression="Erlotinib,0,,bar,A2M,"/>
                    <has_text_matching expression="Erlotinib,0,,bar,ABCC4,"/>
                    <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.predicted_labels">
                <assert_contents>
                    <has_text_matching expression="source_dataset:A-704,Erlotinib,"/>
                    <has_text_matching expression="target_dataset:KMRC-20,Erlotinib,"/>
                </assert_contents>
            </element>
            <element name="job.stats">
                <assert_contents>
                    <has_text_matching expression="DirectPred,Erlotinib,numerical,mse,"/>
                    <has_text_matching expression="DirectPred,Erlotinib,numerical,r2,"/>
                    <has_text_matching expression="DirectPred,Erlotinib,numerical,pearson_corr,"/>
                </assert_contents>
            </element>
        </output_collection>
    </xml>
    <token name="@COMMON_HELP@">

4:07f018886d40

<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/>

        <param name="non_commercial_use" label="I certify that I am not using this tool for commercial purposes." type="boolean" truevalue="NON_COMMERCIAL_USE" falsevalue="COMMERCIAL_USE" checked="False">
            <validator type="expression" message="This tool is only available for non-commercial use.">value == True</validator>
        </param>
    </xml>
    <xml name="main_inputs">
        <param name="train_clin" type="data" format="tabular" label="Training clinical data"/>
        <param name="test_clin" type="data" format="tabular" label="Test clinical data"/>
        <param name="train_omics_main" type="data" format="tabular" label="Training omics data"/>
        <param name="test_omics_main" type="data" format="tabular" label="Test omics data"/>
        <param name="assay_main" type="text" optional="true" label="What type of assay is your input?" help="This would be used as output name.">
            <expand macro="sanitizer_letters"/>
        </param>
    </xml>
    <xml name="extra_inputs">
        <param name="train_omics" type="data" optional="true" format="tabular" label="Training omics data"/>
        <param name="test_omics" type="data" optional="true" format="tabular" label="Test omics data"/>
        <param name="assay" type="text" optional="true" label="What type of assay is your input?" help="This would be used as output name." >
            <expand macro="sanitizer_letters"/>
        </param>
    </xml>
    <xml name="advanced">

        </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"/>
    </xml>
    <token name="@PLOT_COMMON_CONFIG@"><![CDATA[
label_data = load_labels('inputs/$plot_conditional.labels.element_identifier.$plot_conditional.labels.ext')
    ]]></token>
    <token name="@PR_ROC_BOX_CONFIG@"><![CDATA[

    ]]></token>
    <xml name="common_test">
        <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>
            <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/>

                    <has_n_lines n="50"/>
                </assert_contents>
            </element>
            <element name="job.feature_importance.GradientShap">
                <assert_contents>
                    <has_text_matching expression="Erlotinib\t0\t\tbar\tA2M\t"/>
                    <has_text_matching expression="Erlotinib\t0\t\tbar\tABCC4\t"/>
                    <has_text_matching expression="GradientShap"/>
                </assert_contents>
            </element>
            <element name="job.feature_importance.IntegratedGradients">
                <assert_contents>
                    <has_text_matching expression="Erlotinib\t0\t\tbar\tA2M\t"/>
                    <has_text_matching expression="Erlotinib\t0\t\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.predicted_labels">
                <assert_contents>
                    <has_text_matching expression="source_dataset:A-704\tErlotinib\t"/>
                    <has_text_matching expression="target_dataset:KMRC-20\tErlotinib\t"/>
                </assert_contents>
            </element>
            <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@">