<tool id="gcms2isocor" name="Conversion GCMS PostRun Analysis to IsoCor" version="0.1.0" profile="21.05">
    <requirements>
        <requirement type="package" version="8.0.121">openjdk</requirement> 
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
      java -jar '$__tool_directory__/P2M2WorkflowsTools-assembly-0.1.jar' 
       #for $input in $input_gcms_files
         #if $input
           $input
         #end if
        #end for
        --out '$output_isocor'
    ]]></command>
    <inputs>
        <param type="data" name="input_gcms_files" multiple="true" format="txt" />
    </inputs>
    <outputs>
        <data name="output_isocor" format="tsv" />
    </outputs>
    <tests>
        <test>
            <param name="input_gcms_files" value="13CPROT1.txt,13CPROT2.txt"/>
            <output name="output_isocor" file="input_isocor.tsv"/>
        </test>
    </tests>
    <help><![CDATA[
        Conversion from GCMS PostRun Analysis to Isocore.
	Processes GCMS files with the following categories: Header, MS Quantitative Results.
    ]]></help>
</tool>