<tool id="influx_data_manager" name="Influx Data Connector: Handling influx_si data inputs in Galaxy workflows" version="@TOOL_VERSION@+galaxy0" profile="23.0">
    <macros>
        <token name='@TOOL_VERSION@'>1.0.0</token>
    </macros>
    <requirements>
        <requirement type='package' version='@TOOL_VERSION@'>influx-si-data-manager</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
    influx_data_manager
    --physiofit '$physiofit' 
    --isocor '$isocor'
    --linp '$linp'
    --netw '$netw'
    --mmet '$mmet'
    --cnstr '$cnstr' 
    --tvar '$tvar'
    --opt '$opt'
    --log '$stdout'
    $verbose
    2> '$stderr' && cat '$stdout'
    ]]></command>
    <inputs>
        <param type='data' format='tabular,txt' argument='--netw' label='File containing network for experiments (.netw file)' optional='false'/>
        <param type='data' format='tabular,txt' argument='--isocor' label='Output of isocor which corresponds to the .miso input (.tsv file)' optional='false'/>
        <param type='data' format='tabular,txt' argument='--tvar' label='File containing types of variables for experiments (.tvar file)' optional='false'/>
        <param type='data' format='tabular,txt' argument='--physiofit' label='Output of physiofit which corresponds to the .mflux input (.csv file)' optional='true'/>
        <param type='data' format='tabular,txt' argument='--linp' label='File contianing label inputs for experiments (.linp file)' optional='true'/>
        <param type='data' format='tabular,txt' argument='--mmet' label='File containing specie concentrations for experiments (.mmet file)' optional='true'/>
        <param type='data' format='tabular,txt' argument='--cnstr' label='File containing constraints onf fluxes and specie concentrations for experiments (.constr file)' optional='true'/>
        <param type='data' format='tabular,txt' argument='--opt' label='File containing options for influx_si (.opt  file)' optional='true'/>
        <param name='verbose' type='boolean' truevalue='--verbose' falsevalue='' label='Debug mode' help='Select "Yes" to have debug logs be printed out'/>
    </inputs>
    <outputs>
        <data format='txt' name='stdout' label='Run log'/>
        <collection type='list' label='Influx_si input files' name='list_output'>
            <discover_datasets pattern='__name_and_ext__' format='zip'/>
        </collection>
        <data format='txt' name='stderr' label='Influx DM error log'/>
    </outputs>
    <tests>
        <test expect_num_outputs='3'>
            <param name='netw'  value='galaxy_test.netw'/>
            <param name='isocor' value='galaxy_test.tsv'/>
            <param name='tvar' value='galaxy_test.tvar'/>
            <param name='physiofit' value='galaxy_test.csv'/>
            <param name='linp' value='galaxy_test.linp'/>
            <!-- <param name='in_mmet' value='galaxy_test.mmet'/> FOR FUTURE USE IN INSTATIONARY SETTING -->
            <param name='cnstr' value='galaxy_test.cnstr'/>
            <param name='opt' value='galaxy_test.opt'/>
            <param name='verbose' value='true'/>
            <output_collection name='list_output' type='list'>
                <element name='Sample_1'>
                    <assert_contents>
                        <has_archive_member path='Sample_1.miso'>
                            <has_text_matching expression='sample\tId\tComment\tSpecie\tFragment\tDataset\tIsospecies\tSD\tTime'/>
                            <has_n_lines n='30'/>
                        </has_archive_member>
                        <has_archive_member path='Sample_1.mflux'>
                            <has_text_matching expression='Id\tComment\tFlux\tValue\tSD'/>
                            <has_text_matching expression='Glc_q'/>
                            <has_n_lines n='4'/>
                        </has_archive_member>
                        <has_archive_member path='Sample_1.netw'>
                            <has_n_lines n='87'/>
                        </has_archive_member>
                        <has_archive_member path='Sample_1.tvar'/>
                        <has_archive_member path='Sample_1.linp'/>
                        <has_archive_member path='Sample_1.cnstr'/>
                        <has_archive_member path='Sample_1.opt'/>
                    </assert_contents>
                </element>
            </output_collection>
        </test>
    </tests>
    <help><![CDATA[
    This tool is meant to handle the input files for influx_si within workflows. It is not meant to be used as a stand-alone within the platform.
    ]]></help>
    <citations>
        <citation type='bibtex'>
            @misc{
            githubinflux_si,
            author = {Le Gregam, Loic},
            year = {2024},
            title = {Influx-si-data-manager},
        }
        </citation>
        </citations>
</tool>