<tool id="openlabcds2csv" name="Converting multiple OpenLabCDS Text Files to a CSV summary file" 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 -cp '$__tool_directory__/P2M2WorkflowsTools-assembly-0.1.4.jar' fr.inrae.metabolomics.p2m2.OpenLabCDS2CsvCommand
       #for $input in $input_openlabscds_files
         #if $input
           $input
         #end if
        #end for
        --out '$output_csv' --column '$column'
    ]]></command>
    <inputs>
        <param type="data" name="input_openlabscds_files" multiple="true" format="txt" />
        <param type="select" name="column" label="target column to build as summary">
    		<option value="RetTime">RetTime</option>
    		<option value="Type">Type</option>
    		<option value="ISTD">ISTD</option>
    		<option value="Area" selected="true">Area</option>
    		<option value="Amt/Area">Amt/Area</option>
    		<option value="Amount">Amount</option>
            <option value="Grp">Grp</option>
        </param>
    </inputs>
    <outputs>
        <data name="output_csv" format="csv" />
    </outputs>
    <tests>
        <test>
            <param name="input_openlabscds_files" value="Report_Ex1.txt,Report_Ex2.txt,Report_Ex3.txt"/>
            <param name="column" value="Area"/>
            <output name="output_csv" file="Results.csv"/>
        </test>
    </tests>
    <help><![CDATA[
       Get multiple "Internal Standard Report" from the OpenLabCDS software where are describe a list of compound in format row (columns : RetTime  Type  ISTD    Area     Amt/Area    Amount   Grp   Name)
       The converter creates a summary that contains a header (a list of compounds) and a list of "Sample name" with associated values ​​for a target column (RetTime,Type,ISTD,Area,Amt/Area,Amount,Grp,Name)
    ]]></help>
</tool>