<tool id="recetox_aplcms_recover_weaker_signals" name="RECETOX apLCMS - recover weaker signals" version="@TOOL_VERSION@+galaxy0">
    <description>recover weaker signals from LC/MS spectra</description>
    <macros>
        <import>macros.xml</import>
        <import>macros_split.xml</import>
    </macros>
    <expand macro="creator"/>

    <expand macro="requirements"/>
    <command detect_errors="aggressive"><![CDATA[
        sh ${symlink_inputs} &&
        Rscript -e 'source("${__tool_directory__}/utils.R")' -e 'source("${__tool_directory__}/main.R")' -e 'source("${run_script}")'
    ]]></command>
    <configfiles>
        <configfile name="symlink_inputs">
            #for $infile in $ms_files
                ln -s '${infile}' '${infile.element_identifier}'
            #end for
            #for $infile in $extracted_files
                ln -s '${infile}' '${infile.element_identifier}'
            #end for
            #for $infile in $corrected_files
                ln -s '${infile}' '${infile.element_identifier}'
            #end for
        </configfile>
        <configfile name="run_script"><![CDATA[
            #set filenames = str("', '").join([str($f.element_identifier) for $f in $ms_files])
            filenames <- sort_samples_by_acquisition_number(c('$filenames'))

            #set extracted_files = str("', '").join([str($f.element_identifier) for $f in $extracted_files])
            extracted <- load_features(c('$extracted_files'))

            #set corrected_files = str("', '").join([str($f.element_identifier) for $f in $corrected_files])
            corrected <- load_features(c('$corrected_files'))

            aligned <- load_aligned_features('$rt_cross_table_file', '$int_cross_table_file', '$tolerances_file')

            cluster <- as.integer(Sys.getenv('GALAXY_SLOTS', unset = 1))

            recovered <- recover_signals(cluster,
                                         filenames,
                                         extracted,
                                         corrected,
                                         aligned,
                                         $mz_tol,
                                         $weak_signal_recovery.recover_mz_range,
                                         $weak_signal_recovery.recover_chr_range,
                                         $weak_signal_recovery.use_observed_range,
                                         $min_bandwidth,
                                         $max_bandwidth,
                                         $weak_signal_recovery.recover_min_count
            )

            aligned_feature_sample_table <- create_feature_sample_table(aligned)
            recovered_feature_sample_table <- create_feature_sample_table(recovered)

            save_all_features(recovered, filenames)
            save_all_feature_tables(aligned_feature_sample_table, recovered_feature_sample_table,
                                    '${aligned_feature_sample_table}', '${recovered_feature_sample_table}',
                                    '$output_format.out_format')
        ]]></configfile>
    </configfiles>

    <inputs>
        <param name="ms_files" type="data" format="mzdata,mzml,mzxml,netcdf" multiple="true" min="2" label="Input data"
               help="Mass spectrometry file for peak extraction." />
        <param name="extracted_files" type="data" format="parquet" multiple="true" min="2" label="Input extracted feature samples"
               help="Mass spectrometry files containing feature samples." />
        <param name="corrected_files" type="data" format="parquet" multiple="true" min="2" label="Input corrected feature samples"
               help="Mass spectrometry file containing corrected feature samples." />
        <param name="tolerances_file" type="data" format="parquet" label="Input tolerances" help="TBD"/>
        <param name="rt_cross_table_file" type="data" format="parquet" label="Input rt cross table" help="TBD"/>
        <param name="int_cross_table_file" type="data" format="parquet" label="Input int cross table" help="TBD"/>
        <expand macro="mz_tol_macro"/>
        <param name="min_bandwidth" type="float" optional="true" label="min_bandwidth (optional)"
               help="The minimum bandwidth to use in the kernel smoother." />
        <param name="max_bandwidth" type="float" optional="true" label="max_bandwidth (optional)"
               help="The maximum bandwidth to use in the kernel smoother." />
        <expand macro="weak_signal_recovery"/>
        <expand macro="output_format"/>
    </inputs>

    <outputs>
        <expand macro="unsupervised_outputs">
            <collection  name="extracted_features" type="list" label="${tool.name} extracted_features on ${on_string}">
                <discover_datasets pattern="__designation__" directory="extracted" format="parquet" />
            </collection >
            <collection  name="corrected_features" type="list" label="${tool.name} corrected_features on ${on_string}">
                <discover_datasets pattern="__designation__" directory="corrected" format="parquet" />
            </collection >
        </expand>
    </outputs>

    <tests>
        <test>
            <param name="ms_files" value="mbr_test2.mzml,mbr_test1.mzml,mbr_test0.mzml" ftype="mzml"/>
            <param name="extracted_files" ftype="parquet"
                   value="extracted_expected/extracted_0.parquet,extracted_expected/extracted_1.parquet,extracted_expected/extracted_2.parquet"/>
            <param name="corrected_files" ftype="parquet"
                   value="corrected_expected/corrected_0.parquet,corrected_expected/corrected_1.parquet,corrected_expected/corrected_2.parquet"/>
            <param name="tolerances_file" value="tolerances.parquet" ftype="parquet"/>
            <param name="rt_cross_table_file" value="rt_cross_table.parquet" ftype="parquet"/>
            <param name="int_cross_table_file" value="int_cross_table.parquet" ftype="parquet"/>

            <output name="recovered_feature_sample_table" ftype="parquet"
                    file="unsupervised_output/unsupervised_recovered_feature_sample_table.parquet"/>
            <output name="aligned_feature_sample_table" ftype="parquet"
                    file="unsupervised_output/unsupervised_aligned_feature_sample_table.parquet"/>
            <output_collection name="corrected_features" type="list">
                <element name="mbr_test0.parquet" file="unsupervised_output/corrected_features_0.parquet" ftype="parquet"/>
                <element name="mbr_test1.parquet" file="unsupervised_output/corrected_features_1.parquet" ftype="parquet"/>
                <element name="mbr_test2.parquet" file="unsupervised_output/corrected_features_2.parquet" ftype="parquet"/>
            </output_collection>
            <output_collection name="extracted_features" type="list">
                <element name="mbr_test0.parquet" file="unsupervised_output/extracted_features_0.parquet" ftype="parquet"/>
                <element name="mbr_test1.parquet" file="unsupervised_output/extracted_features_1.parquet" ftype="parquet"/>
                <element name="mbr_test2.parquet" file="unsupervised_output/extracted_features_2.parquet" ftype="parquet"/>
            </output_collection>
        </test>
    </tests>

    <help>
        <![CDATA[
            This is a tool which runs apLCMS recovery of weaker signals.

            @GENERAL_HELP@
        ]]>
    </help>

    <expand macro="citations"/>
</tool>