view aplcms_unsupervised.xml @ 3:de4a15f108a1 draft default tip

"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ffadabe63b4a1428918cb80dc1f8598f41a458bd"

<tool id="aplcms_unsupervised" name="apLCMS - Unsupervised" version="@TOOL_VERSION@+galaxy3">
    <macros>
        <import>aplcms_macros.xml</import>
    </macros>

    <expand macro="requirements" />

    <command detect_errors="aggressive"><![CDATA[
        Rscript ${run_script}
    ]]></command>

    <configfiles>
        <configfile name="run_script"><![CDATA[
            #set file_str = str("', '").join([str($f) for $f in $files])

            x <- apLCMS::unsupervised(
                files = c('$file_str'),
                min_exp = $noise_filtering.min_exp,
                min_pres = $noise_filtering.min_pres,
                min_run = $noise_filtering.min_run,
                mz_tol = $noise_filtering.mz_tol,
                baseline_correct = $noise_filtering.baseline_correct,
                baseline_correct_noise_percentile = $noise_filtering.baseline_correct_noise_percentile,
                intensity_weighted = $noise_filtering.intensity_weighted,
                shape_model = '$feature_detection.shape_model',
                BIC_factor = $feature_detection.BIC_factor,
                peak_estim_method = '$feature_detection.peak_estim_method',
                min_bandwidth = $feature_detection.min_bandwidth,
                max_bandwidth = $feature_detection.max_bandwidth,
                sd_cut = c($feature_detection.sd_cut_min, $feature_detection.sd_cut_max),
                sigma_ratio_lim = c($feature_detection.sigma_ratio_lim_min, $feature_detection.sigma_ratio_lim_max),
                component_eliminate = $feature_detection.component_eliminate,
                moment_power = $feature_detection.moment_power,
                align_chr_tol = $peak_alignment.align_chr_tol,
                align_mz_tol = $peak_alignment.align_mz_tol,
                max_align_mz_diff = $peak_alignment.max_align_mz_diff,
                recover_mz_range = $weak_signal_recovery.recover_mz_range,
                recover_chr_range = $weak_signal_recovery.recover_chr_range,
                use_observed_range = $weak_signal_recovery.use_observed_range,
                recover_min_count = $weak_signal_recovery.recover_min_count,
                cluster = as.integer(Sys.getenv('GALAXY_SLOTS', unset = 1))
            )

            apLCMS::save_peaks_to_hdf('$peaks', x)
        ]]></configfile>
    </configfiles>

    <expand macro="inputs">
        <expand macro="noise_filtering" />
        <expand macro="feature_detection" />
        <expand macro="peak_alignment" />
        <expand macro="weak_signal_recovery" />
    </expand>

    <outputs>
        <data name="peaks" format="h5" />
    </outputs>

    <tests>
        <test>
            <param name="files" value="mbr_test0.mzml,mbr_test1.mzml,mbr_test2.mzml" ftype="mzml"/>
            <output name="peaks" file="peaks_unsupervised.h5" ftype="h5" compare="sim_size" delta="1000"/>
        </test>
    </tests>

    <help>
        This is the Unsupervised version of apLCMS which is not relying on any existing knowledge about metabolites or
        any historically detected features. For such functionality please use the Hybrid version of apLCMS.

        @GENERAL_HELP@
    </help>

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