annotate mztabm_validate.xml @ 0:520706977927 draft default tip

planemo upload for repository https://github.com/RECETOX/galaxytools/tree/main/tools/mztabm commit 9e8dabb356b4d26714194c1a5506c6fedb07d8d8

<tool id="mztabm_validate" name="mztab-m validate" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0" license="MIT">
    <description>validate mztab-m files</description>
    <macros>
        <token name="@TOOL_VERSION@">1.0.6</token>
        <token name="@VERSION_SUFFIX@">0</token>
    </macros>

    <xrefs>
        <xref type="bio.tools">jmztab-m</xref>
    </xrefs>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">jmztab-m</requirement>
    </requirements>

    <command detect_errors="exit_code"><![CDATA[
        jmztab-m --level $level -c '$input_file' -o '$output_file' $checkSemantic
    ]]></command>
    <inputs>
        <param name="input_file" type="data" format="mztab,txt,json" label="Input file" help="The mzTab-M or plain text file to be validated. mzTab-M is a standard format for reporting metabolomics results." />
        <param name="level" type="select" label="Level" help="Select the validation level: Info (all messages), Warn (warnings and errors), or Error (only errors).">
            <option value="Info" selected="true">Info</option>
            <option value="Warn">Warn</option>
            <option value="Error">Error</option>
        </param>
        <param argument="--checkSemantic" type="boolean" truevalue="--checkSemantic" falsevalue="" checked="false" label="Check semantic validation" help="If enabled, performs additional semantic validation checks on the input file." />
    </inputs>
    <outputs>
        <data name="output_file" format="txt" label="${tool.name} on ${on_string}" />
    </outputs>
    <tests>
        <!-- Hint: You can use [ctrl+alt+t] after defining the inputs/outputs to auto-scaffold some basic test cases. -->
    <test expect_num_outputs="1">
        <!--TODO: auto-generated test case. Please fill in the required values-->
        <param name="input_file" value="MTBLS263.mztab" ftype="mztab"/>
        <param name="checkSemantic" value="false"/>
        <param name="level" value="Info"/>
        <output name="output_file">
            <assert_contents>
                <has_text text="commit: '5fee003a3c97695b422bf556f4b5d9eb24080a3c'"/>
                <has_line line="Validator set to level 'Info'"/>
                <has_n_lines n="16"/>
            </assert_contents>
        </output>
    </test>
    </tests>
    <help><![CDATA[
.. class:: infomark

**What it does**

This tool validates mzTab-M files using the jmztab-m validator. mzTab-M is a standardized tabular format for reporting metabolomics results, including identification and quantification data. The validator checks the file for format compliance and, optionally, for semantic correctness.

Usage
.....

1. **Input**
    - Provide an mzTab-M or plain text file to be validated.
    - Optionally enable semantic validation for deeper checks.
    - Choose the desired validation level:
        - **Info**: Show all messages (informational, warnings, errors).
        - **Warn**: Show only warnings and errors.
        - **Error**: Show only errors.

2. **Output**
    - A plain text report summarizing the validation results, including any detected issues.

**Parameters**

- **Input file**: The mzTab-M or text file to validate.
- **Check semantic validation**: Enable to perform additional semantic checks.
- **Level**: Controls the strictness of the validation output.
    ]]></help>
    <citations>
        <citation type="doi">10.5281/zenodo.3662402</citation>
        <citation type="doi">10.1021/acs.analchem.8b04310</citation>
        <citation type="doi">10.1021/acs.analchem.9b01987</citation>
    </citations>
</tool>