comparison mfassignr_histnoise.xml @ 0:faf7108f3b48 draft

planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr commit 87bb82e07c57753a71d9ce4efc757c4367200d15

0:faf7108f3b48

<tool id="mfassignr_histnoise" name="MFAssignR HistNoise" version="@TOOL_VERSION@+galaxy0" profile="23.0">
    <description>Noise level assessment using the HistNoise</description>
    <macros>
        <import>macros.xml</import>
        <import>help.xml</import>
    </macros>
    <edam_topics>
        <edam_topic>topic_3172</edam_topic>    
    </edam_topics>
    <expand macro="creator" />
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[
        Rscript '${run_script}'
    ]]></command>
    <configfiles>
        <configfile name="run_script"><![CDATA[
        df <- read.delim("$input_file", sep="\t")
        assess_noise <- MFAssignR::HistNoise(
            df = df,
            SN = $SN,
            bin = $bin
        )
        noise <- assess_noise[['Noise']]
        write.table(noise, file = '$Noise', row.names= FALSE, col.names = FALSE)
        ggplot2::ggsave(filename = "histplot.png", assess_noise[['Hist']])
        ]]></configfile>
    </configfiles>
    <inputs>
        <expand macro="histnoise_param"/>
    </inputs>
    <outputs>
        <data name="Noise" format="txt" label="Noise level estimate by ${tool.name} on ${on_string}"/>
        <data name="Hist_plot" format="png" label="Histogram plot by ${tool.name} on ${on_string}" from_work_dir="histplot.png"/>
    </outputs>
    <tests>
        <test>
            <param name="input_file" value="QC1_1_POS_500.tabular" />
            <output name="Noise" ftype="txt">
                <assert_contents>
                    <has_text text="674849323.854921" />
                </assert_contents>
            </output>
            <output name="Hist_plot" ftype="png" file="histnoise/plot.png">
            </output>
        </test>
    </tests>
    <help><![CDATA[
        @HISTNOISE_HELP@

        @GENERAL_HELP@
    ]]></help>
    <expand macro="citations" />
</tool>