<tool id='skyline2isocor' name='Skyline2Isocor: converting skyling outputs into IsoCor inputs' version='@TOOL_VERSION@+galaxy0' profile='20.5'>
    <macros>
        <token name='@TOOL_VERSION@'>1.0.0</token>
    </macros>
    <requirements>
        <requirement type='package' version='@TOOL_VERSION@'>skyline2isocor</requirement>
    </requirements>
    <command detect_errors='exit_code'><![CDATA[
    skyline2isocor -i '$skyline_output' -o '$isocor_input' > '$stdout' 2> '$stderr'
    ]]></command>
    <inputs>
        <param type='data' format='tabular, txt' name='skyline_output' label='Skyline output file' help='Skyline output to convert'/>
    </inputs>
    <outputs>
        <data format='txt' name='stdout' label='Log'/>
        <data format='txt' name='stderr' label='Error log' />
        <data format='tabular,txt' name='isocor_input' label='IsoCor input file' />
    </outputs>
    <tests>
        <test>
            <param name='skyline_output' value='skyline_output.txt' />
            <output name='isocor_input' value='test_output.tsv' />
        </test>
    </tests>
    <help><![CDATA[
        Preparing skyline output data for use in IsoCor software for natural abundance isotope correction. Can be directly linked to Isocor in a workflow.
        Input is the skyline output. Necessary columns: File Name, Molecule Name, Product Adduct, Total Area.
        ]]></help>
    <citations>
        <citation type='bibtex'>
                @misc{
                githubskyline2isocor,
                author = {Le Gregam, Loic},
                year = {2024},
                title = {Skyline2IsoCor,
            }
        </citation>
    </citations>
</tool>