<tool id="mzml_validator" name="mzML Schema Validator" version="0.1.0+galaxy2" profile="21.05">
    <description>validates mzML files against XML Schema Definition (XSD)</description>
    <creator>
        <person
            givenName="Maksym"
            familyName="Skoryk"
            url="https://github.com/maximskorik"
            identifier="0000-0003-2056-8018" />
        <organization
            url="https://www.recetox.muni.cz/"
            email="GalaxyToolsDevelopmentandDeployment@space.muni.cz"
            name="RECETOX MUNI" />
    </creator>

    <requirements>
        <requirement type="package" version="4.9.1">lxml</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        python3 '${__tool_directory__}/mzml_validator_wrapper.py'
        --input_file '$input'
        --schemas_dir '${__tool_directory__}/schemas'
        --xsd_versions $xsd_versions
        --log_file '$log'
        ]]></command>
    <inputs>
        <param name="input" type="data" format="mzml" label="Input mzML file"/>
        <param name="xsd_versions" type="select" label="Schema version to validate against" multiple="true" display="checkboxes"
            help="select XML schema definition (XSD) version to validate the file against. If both are selected, a file is valid if matches against any of the versions.">
            <option value="1.1.1">1.1.1</option>
            <option value="1.1.0">1.1.0</option>
        </param>
    </inputs>
    <outputs>
        <data name="log" format="txt" label="mzML Validation on ${on_string}" />
    </outputs>
    <tests>
        <test> <!-- test 1: validate mzML 1.1.1 against both XSDs  -->
            <param name="input" value="small_pwiz_1.1.1_truncated.mzML" />
            <param name="xsd_versions" value="1.1.0,1.1.1" />
            <output name="log">
                <assert_contents>
                    <has_text text="Validated against mzML XML Schema Definition v1.1.1" />
                </assert_contents>
            </output>
        </test>
        <test expect_failure="true" expect_exit_code="1"> <!-- test 2: try validate mzML 1.1.1 against XSD v1.1.0 -->
            <param name="input" value="small_pwiz_1.1.1_truncated.mzML" />
            <param name="xsd_versions" value="1.1.0" />
            <assert_stderr>
                <has_text text="Failed to validate against mzML XML Schema Definition v1.1.0" />
            </assert_stderr>
        </test>
        <test expect_failure="true" expect_exit_code="1"> <!-- test 3: validate corrupted mzML -->
            <param name="input" value="mbr_truncated.mzml" />
            <param name="xsd_versions" value="1.1.0,1.1.1" />
            <assert_stderr>
                <has_text text="Failed to validate against mzML XML Schema Definition v1.1.0" />
                <has_text text="Failed to validate against mzML XML Schema Definition v1.1.1" />
            </assert_stderr>
        </test>
    </tests>
    <help><![CDATA[
        **mzML Schema Validator** validates mzML files against XML Schema Definition (XSD) developed by HUPO Proteomics Standard Initiative
        (https://www.psidev.info/mzML).
    ]]></help>

    <citations>
        <citation type="doi">https://doi.org/10.5281/zenodo.6035335</citation>
    </citations>
</tool>