<tool id="presto_parselog" name="pRESTO ParseLog" version="@PRESTO_VERSION@">
    <description>Create tabular report from pRESTO log file</description>
    
    <macros>
        <import>presto_macros.xml</import>
    </macros>
    
    <expand macro="requirements"/>
    
    <version_command>ParseLog.py --version</version_command>
    <command detect_errors="exit_code"><![CDATA[
        ParseLog.py 
          -l '$log_file'
          -f $fields
          --outdir=.
          --outname=tmp
    ]]></command>

    <inputs>
        <param argument="-l" name="log_file" type="data" format="txt" label="pRESTO log file" help="Detailed log file generated from a pRESTO tool."/>
        <param argument="-f" name="fields" type="text" label="Field(s)" help="Space-separated list of fields to extract.">
            <expand macro="text-regex-validator"/>
        </param>
    </inputs>

    <outputs>
        <data name="output" format="tsv" from_work_dir="tmp_table.tab"/>
    </outputs>
    
    <tests>
        <test>
            <param  name="log_file" value="presto_parselog_test_in.txt"/>
            <param  name="fields" value="ID QUALITY"/>
            <output name="output" file="presto_parselog_test_out.txt" sort="true"/>
        </test>
    </tests>
    
    <help><![CDATA[
Creates tab-separated tabular reports from pRESTO detailed log files.

See the `pRESTO online help <@PRESTO_BASE_URL@/en/stable>`_ for more information.

@HELP_NOTE@
    ]]></help>
    <expand macro="citations" />
</tool>