comparison recetox_aplcms_remove_noise.xml @ 9:ffbabefbd2e2 draft

planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b88eaca14b030fc0023989f3c83479e4975d172a

8:b5a1f35abd8a

<tool id="recetox_aplcms_remove_noise" name="recetox-aplcms - remove noise" version="@TOOL_VERSION@+galaxy3" profile="21.09">
    <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>

                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>

    <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@

9:ffbabefbd2e2

<tool id="recetox_aplcms_remove_noise" name="recetox-aplcms - remove noise" version="@TOOL_VERSION@+galaxy0" profile="21.09">
    <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>

                mz_tol = ${mz_tol}/1e6,
                baseline_correct = $baseline_correct,
                baseline_correct_noise_percentile = 0.05,
                intensity_weighted = $intensity_weighted,
                do.plot = FALSE,
                cache = FALSE,
                grouping_threshold = as.numeric('$grouping_threshold')
            )

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

    <tests>
        <test>
            <param name="input_file" value="mbr_test0.mzml" ftype="mzml"/>
            <output name="output_file" file="remove_noise_docker.parquet" ftype="parquet" />
        </test>
        <test>
            <param name="input_file" value="mbr_test0.mzml" ftype="mzml"/>
            <param name="grouping_threshold" value="2" />
            <output name="output_file" file="remove_noise_docker_threshold.parquet" ftype="parquet" />
        </test>
    </tests>

    <help>
        <![CDATA[
            @REMOVE_NOISE_HELP@