<tool id="recetox_aplcms_align_features" name="RECETOX apLCMS - align features" version="@TOOL_VERSION@+galaxy0">
    <description>align features from LC/MS spectra across samples</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("${run_script}")'
    ]]></command>
    <configfiles>
        <configfile name="symlink_inputs">
            #for $infile in $ms_files
                ln -s '${infile}' '${infile.element_identifier}'
            #end for
             #for $infile in $corrected_files
                ln -s '${infile}' '${infile.element_identifier}'
            #end for
        </configfile>
        <configfile name="run_script"><![CDATA[
            #set filenames_str = str("', '").join([str($f.element_identifier) for $f in $ms_files])
            files_list <- sort_samples_by_acquisition_number(c('$filenames_str'))
            sample_names <- get_sample_name(files_list)

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

            aligned <- align_features(
                sample_names = sample_names,
                features = corrected_features,
                min.exp = $min_exp,
                mz.tol = $peak_alignment.align_mz_tol,
                chr.tol = $peak_alignment.align_chr_tol,
                find.tol.max.d = 10 * $mz_tol,
                max.align.mz.diff = $peak_alignment.max_align_mz_diff,
                do.plot = FALSE
            )

            save_aligned_features(aligned, "$rt_cross_table", "$int_cross_table", "$tolerances")
        ]]></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="corrected_files" type="data" format="parquet"  multiple="true" min="2"
               label="Input corrected feature samples"
               help="Mass spectrometry files containing corrected feature samples." />
        <expand macro="mz_tol_macro"/>
        <param name="min_exp" type="integer" min="1" value="2" label="min_exp"
               help="If a feature is to be included in the final feature table, it must be present in at least this number of spectra." />
        <expand macro="peak_alignment"/>
    </inputs>

    <outputs>
        <data name="tolerances" format="parquet" label="${tool.name} on ${on_string} (tolerances)" />
        <data name="rt_cross_table" format="parquet" label="${tool.name} on ${on_string} (rt cross table)" />
        <data name="int_cross_table" format="parquet" label="${tool.name} on ${on_string} (int cross table)" />
    </outputs>

    <tests>
        <test>
            <param name="ms_files" value="mbr_test0.mzml,mbr_test1.mzml,mbr_test2.mzml" ftype="mzml"/>
            <param name="corrected_files" ftype="parquet"
                   value="corrected_expected/corrected_0.parquet,corrected_expected/corrected_1.parquet,corrected_expected/corrected_2.parquet"/>
            <output name="tolerances" file="tolerances.parquet" ftype="parquet"/>
            <output name="rt_cross_table" file="rt_cross_table.parquet" ftype="parquet"/>
            <output name="int_cross_table" file="int_cross_table.parquet" ftype="parquet"/>
        </test>
    </tests>

    <help>
        <![CDATA[
            This is a tool which runs apLCMS alignment of features.

            @GENERAL_HELP@
        ]]>
    </help>

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