<tool id="gcms2isocor" name="Conversion GCMS PostRun Analysis to IsoCor" version="0.1.0" profile="20.09">
    <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="tabular" />
    </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[
        Convert the GC-MS raw data input files into a unique table suitable as input file for IsoCor.
	
	Processes GCMS files should be exported with the following categories: [Header], [MS Quantitative Results].
	GC-MS raw dataset should contains a column "Name" filled with each carbon isotopologue of each fragment considered and a column "Area" filled with the area of the integrated peak. 
	The name of each fragment must be written exactly as specified in the "Metabolite.dat" file (see https://isocor.readthedocs.io/en/latest/tutorials.html#input-data) to ensure accurate correction with
	IsoCor. 

	Example: the name “ProlineC2C5_TMS_m0” is for the GC-MS fragment m/z 142 (integrated peak) containing the C2-C3-C4-C5 carbon skeleton of proline and 1 TMS derivative. m0 refers to the carbon isotopologue
	monitored (m0 for m/z = 142, m1 for m/z = 143, m2 for m/z = 144, m3 for m/z = 145, m4 for m/z = 146).
    ]]></help>
</tool>