annotate waveica.xml @ 0:328710890963 draft

"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"

<tool id="waveica" name="WaveICA" version="@TOOL_VERSION@+galaxy1" python_template_version="3.5">
    <description>removal of batch effects for untargeted metabolomics data</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="creator"/>

    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">r-recetox-waveica</requirement>
    </requirements>
    <command detect_errors="aggressive"><![CDATA[
        Rscript
            -e 'source("${__tool_directory__}/waveica_wrapper.R")'

            #if $batch_correction.mode == "batchwise":
            -e 'normalized_data <- waveica(
                data = "$data",
                wavelet_filter = "$wf.wavelet_filter",
                wavelet_length = "$wf.wavelet_length",
                k = $k,
                t = $batch_correction.t,
                t2 = $batch_correction.t2,
                alpha = $alpha,
                exclude_blanks = $exclude_blanks
            )'
            #else if $batch_correction.mode == "single_batch":
            -e 'normalized_data <- waveica_singlebatch(
                data = "$data",
                wavelet_filter = "$wf.wavelet_filter",
                wavelet_length = "$wf.wavelet_length",
                k = $k,
                alpha = $alpha,
                cutoff = $batch_correction.cutoff,
                exclude_blanks = $exclude_blanks
            )'
            #end if

            -e 'store_data(normalized_data,"$normalized_data")'
    ]]></command>

    <inputs>
        <expand macro="general_parameters"/>
        <expand macro="wf"/>
        <conditional name="batch_correction">
            <param name="mode" type="select" label="Batch correction mode" help="'multiple batches' takes into account
            inter- and intrabatch intensity drift; 'single batch' relies only on the injection order of the samples and
            requires no batch information [2]">
                <option value="batchwise" selected="true">Multiple batches</option>
                <option value="single_batch">Single batch (or no batch information)</option>
            </param>
            <when value="batchwise">
                <expand macro="batchwise_parameters"/>
            </when>
            <when value="single_batch">
                <expand macro="singlebatch_parameters"/>
            </when>
        </conditional>
        <expand macro="exclude_blanks"/>
    </inputs>

    <expand macro="outputs"/>

    <tests>
        <test>
            <param name="data" value="input_data.csv" ftype="csv"/>
            <param name="mode" value="batchwise"/>
            <param name="wavelet_filter" value="d"/>
            <param name="filter_length" value="2"/>
            <param name="k" value="20"/>
            <param name="t" value="0.05"/>
            <param name="t2" value="0.05"/>
            <param name="alpha" value="0"/>
            <output name="normalized_data" file="normalized_data.tsv"/>
        </test>
        <!-- The following test has different results on three platform I've tried -->
        <!-- <test>
            <param name="data" value="input_data_nobatch.csv" ftype="csv"/>
            <param name="mode" value="single_batch"/>
            <param name="wavelet_filter" value="d"/>
            <param name="filter_length" value="2"/>
            <param name="k" value="20"/>
            <param name="alpha" value="0"/>
            <param name="cutoff" value="0"/>
            <output name="normalized_data" file="normalized_data_nobatch.tsv"/>
        </test> -->
        <test expect_failure="true">
            <param name="data" value="na_data.csv" ftype="csv"/>
        </test>
        <test expect_failure="true">
            <param name="data" value="incomplete_metadata_data.csv" ftype="csv"/>
        </test>
    </tests>

    <help>
        <![CDATA[
        @HELP@
        ]]>
    </help>

    <citations>
        <citation type="doi">10.1016/j.aca.2019.02.010</citation>
        <citation type="doi">10.1007/s11306-021-01839-7</citation>
    </citations>

</tool>