<tool id="use_theoretical_mz" name="use theoretical m/z values" version="@TOOL_VERSION@+galaxy4" profile="21.09">
    <description>Overwrite experimentally measured mz values for peaks with theoretical values from peak comments.</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="creator"/>

    <command detect_errors="exit_code"><![CDATA[
    python '$__tool_directory__/use_theoretical_mz_annotations.py'
    -i '${input}'
    -o '${output_data}' 
    #if $only_theoretical_annotated
    -a
    #end if
    ]]>
    </command>

    <inputs>
        <param name="input" type="data" format="msp,mgf" label="Input mass spectral library with peak comments in RIKEN format." />
        <param name="only_theoretical_annotated" type="boolean" label="only retain annotated peaks" truevalue="True" falsevalue="False" checked="false" />
    </inputs>

    <outputs>
        <data name="output_data" format_source="input" />
    </outputs>

    <tests>
        <test>
            <param name="input" value="input.msp" ftype="msp"/>
            <param name="only_theoretical_annotated" value="True"/>
            <output name="output_data" value="output_only_annotated.msp"/>
        </test>
        <test>
            <param name="input" value="input.msp" ftype="msp"/>
            <param name="only_theoretical_annotated" value="False"/>
            <output name="output_data" value="output_plus_no_annotated.msp"/>
        </test>
    </tests>

    <help>
        <![CDATA[
        This tool uses theoretical M/Z annotations in the input MSP or MGF file. 
        You can choose whether to include non-annotated peaks in the output.
        ]]>
    </help>
    <!-- check is this is the correct citation -->
    <citations>
        <citation type="doi">10.21105/joss.04337</citation>
    </citations>
</tool>