annotate macros.xml @ 1:ebb0730f6175 draft default tip

planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools commit 91d32d5b671c523cbe1f47cde279cd8d61826c78

<macros>
    <token name="@TOOL_VERSION@">3.5.1</token>
    <xml name="creator">
        <creator>
            <person
                givenName="Kristina"
                familyName="Gomoryova"
                url="https://github.com/KristinaGomoryova"
                identifier="0000-0003-4407-3917" />
            <person
                givenName="Helge"
                familyName="Hecht"
                url="https://github.com/hechth"
                identifier="0000-0001-6744-996X" />
            <organization
                url="https://www.recetox.muni.cz/"
                email="[e-mail]"
                name="RECETOX MUNI" />
        </creator>
    </xml>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@TOOL_VERSION@">r-ggplot2</requirement>
            <requirement type="package" version="1.3.1">r-tidyr</requirement>
            <requirement type="package" version="19.0.0">r-arrow</requirement>
            <requirement type="package" version="1.1.5">r-rlang</requirement>
        </requirements>
    </xml>

    <xml name="boxplot_param">
       <param name="input_data" type="data" format="csv,tsv,txt,tabular,parquet" label="Input table" help= "Input file in a tabular/tsv/csv/parquet format"/>
        <param name="has_rownames" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Does the first column of input table contain rownames?" help="Whether the first column of the input data table identifies the rownames (e.g. proteinID) - i.e. it is not a part of data matrix to be plotted."/>
        <param name="transform_data" type="select" display="radio" label="Should the quantitative variable be transformed?" optional="false" help="Whether to transform the quantitative variable (e.g. intensity, counts, etc.)">
                <option value="none" selected="true">No transformation</option>
                <option value="replace_zero">Replace zeroes with NA values</option>
                <option value="log2">Log2 transformation</option> 
                <option value="log10">Log10 transformation</option> 
        </param>
        <param name="flip_axes" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Plot the boxplots horizontally? (flip the axes)" help="Whether to flip the axes, so the boxplots will be horizontal instead of vertical."/> 
        <conditional name="grouping_boxplot">
                <param type="select" name="use_grouping" label="Plot boxplot based on a column from the metadata table?" help="Whether to base the boxplot on a different variable than column names (usually corresponding to the samples) from the input table.">
                    <option value="no" selected="true">no</option> 
                    <option value="yes">yes</option>
                </param>     
                <when value="yes">
                    <param name="input_metadata" type="data" format="tabular" label="Input metadata table" help= "Input metadata file in a tabular format"/>
                    <param name="sampleID" type="data_column" data_ref="input_metadata" use_header_names="true" label="Sample identification column in metadata table" help="Column containing sample names - it should correspond to the colNames in the data table."/>
                    <param name="groupingCol" type="data_column" data_ref="input_metadata" use_header_names="true" label="Which variable column to plot on the x-axis?" help="Which column from the metadata table should be plotted on x axis?"/>
                    <param name="colorCol" type="data_column" data_ref="input_metadata" use_header_names="true" label="Color the boxplot based on a variable?" help="Which column from the metadata table should be used for coloring?" optional = "true"/>
                    <param name="facet_x" type="data_column" data_ref="input_metadata" use_header_names="true" label="Column to use as facet on x-axis" optional="true" help="If using faceting, which column should be plotted on x-axis? Default 'Nothing selected' means no faceting will be done on x-axis."/>
                    <param name="facet_y" type="data_column" data_ref="input_metadata" use_header_names="true" label="Column to use as facet on y-axis" optional="true" help="If using faceting, which column should be plotted on y-axis? Default 'Nothing selected' means no faceting will be done on y-axis."/>
                </when>
                <when value="no"/>
        </conditional>  
        <param name="xlab" type="text" label="Label for the x axis" optional="true"/>
        <param name="ylab" type="text" label="Label for the y axis"  optional="true"/>
        <param name="export_R_script" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Export the R script to reproduce the analysis"
                help="Check this box to export the script executed in the Galaxy tool as an R file to be able to reproduce the same processing offline. Not that in this case, the file paths need to be altered and all the dependencies have to be managed manually."/>
    </xml>

    <xml name="citations">
        <citations>
            <citation type="doi">https://doi.org/10.1007/978-0-387-98141-3</citation>
        </citations>        
    </xml>
</macros>