annotate recetox_aplcms_remove_noise.xml @ 4:8fb5e458831f draft

planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 775afc79d12e680bb26496a2626d1855db9cddc7

<tool id="recetox_aplcms_remove_noise" name="recetox-aplcms - remove noise" version="@TOOL_VERSION@+galaxy1">
    <description>filter noise and detect peaks in high resolution mass spectrometry (HRMS) profile data</description>
    <macros>
        <import>macros.xml</import>
        <import>help.xml</import>
    </macros>
    <expand macro="creator"/>
    <expand macro="requirements"/>

    <command detect_errors="aggressive"><![CDATA[
        python '${__tool_directory__}/mzml_id_getter.py' '$input_file';
        Rscript -e 'source("${__tool_directory__}/utils.R")' -e 'source("${run_script}")'
    ]]></command>
    <configfiles>
        <configfile name="run_script"><![CDATA[
            sample_name <- readChar('sample_name.txt', file.info('sample_name.txt')\$size)

            profile <- remove_noise(
                filename = '$input_file',
                min_pres = $min_pres,
                min_run = $min_run,
                mz_tol = ${mz_tol}/1e6,
                baseline_correct = $baseline_correct,
                baseline_correct_noise_percentile = 0.05,
                intensity_weighted = $intensity_weighted,
                do.plot = FALSE,
                cache = FALSE
            )

            profile <- save_sample_name(profile, sample_name)
            save_data_as_parquet_file(profile, '$output_file')
        ]]></configfile>
    </configfiles>

    <inputs>
        <param label="Input spectra data" name="input_file" type="data" format="mzml"
               help="Sample data in .mzml format acquired in profile mode." />
        <expand macro="remove_noise_params"/>
    </inputs>

    <outputs>
        <data label="${($input_file.element_identifier).rsplit('.',1)[0]}.parquet" name="output_file" format="parquet" />
    </outputs>

    <tests>
        <test>
            <param name="input_file" value="mbr_test0.mzml" ftype="mzml"/>
            <output name="output_file" file="remove_noise_docker.parquet" ftype="parquet" />
        </test>
    </tests>

    <help>
        <![CDATA[
            @REMOVE_NOISE_HELP@

            @GENERAL_HELP@
        ]]>
    </help>

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