annotate macros.xml @ 10:1df3b30325dd draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158

<?xml version="1.0"?>
<macros>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@TOOL_VERSION@">r-ggplot2</requirement>
            <yield />
        </requirements>
    </xml>
    <xml name="bio_tools">
        <xrefs>
            <xref type="bio.tools">ggplot2</xref>
        </xrefs>
    </xml>
    <token name="@TOOL_VERSION@">3.5.1</token>
    <token name="@VERSION_SUFFIX@">1</token>

    <token name="@R_INIT@"><![CDATA[
        ## Setup R error handling to go to stderr
        options(show.error.messages=F, error=function(){cat(geterrmessage(), file=stderr()); q("no",1,F)})

        ## Unify locale settings
        loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
    ]]></token>

    <token name="@TRANSFORM@"><![CDATA[
        #if $adv.transform == "log2"
            input["value"] <- log2(input["value"])
        #elif $adv.transform == "log2plus1"
            input["value"] <- log2(input["value"]+1)
        #elif $adv.transform == "log10"
            input["value"] <- log10(input["value"])
        #elif $adv.transform == "log10plus1"
            input["value"] <- log10(input["value"]+1)
        #end if
    ]]></token>

    <token name="@XY_SCALING@"><![CDATA[
        #Choose between automatically scaled x and y axis or user defined
        #if $adv.scaling.plot_scaling == "Automatic"
            gg_scalex = NULL
            gg_scaley = NULL
        #else
            gg_scalex = xlim($adv.scaling.xaxismin, $adv.scaling.xaxismax)
            gg_scaley = ylim($adv.scaling.yaxismin, $adv.scaling.yaxismax)
            cat("\n xaxismin: ", $adv.scaling.xaxismin)
            cat("\n xaxismax: ", $adv.scaling.xaxismax)
            cat("\n yaxismin: ", $adv.scaling.yaxismin)
            cat("\n yaxismax: ", $adv.scaling.yaxismax)
        #end if
    ]]></token>

    <token name="@THEME@"><![CDATA[
        ## Choose theme for plot
        #if $adv.theme == "bw"
            gg_theme = theme_bw()
        #else
            gg_theme = NULL
        #end if
    ]]></token>

    <token name="@LEGEND@"><![CDATA[
        ## Show/hide legend
        #if $adv.legend == "yes"
            gg_legend = theme(legend.position="right")
        #else
            gg_legend = theme(legend.position="none")
            cat("\n no legend")
        #end if
    ]]></token>
    <token name="@SAVE_OUTPUT@"><![CDATA[
        ## output options need to be in out section
        gg_width <- as.double('$out.width_output_dim')
        gg_height <- as.double('$out.height_output_dim')
        gg_unit <- '$out.unit_output_dim'
        gg_dpi <- as.double('$out.dpi_output_dim')
        gg_add_device <- '$out.additional_output_format'
        output1 <- '$output1'
        output2 <- '$output2'

        ## ggsave to png
        ggsave(filename = output1, plot = plot_out, width = gg_width, height = gg_height, units = gg_unit, dpi = gg_dpi, device = "png")
        if(gg_add_device != "none"){
          ggsave(filename = output2, plot = plot_out, width = gg_width, height = gg_height, units = gg_unit, dpi = gg_dpi, device = gg_add_device)
        }
    ]]></token>
    <xml name="read_complex_input">
        <param name="input1" type="data" format="tabular" label="Select table"/>
        <conditional name="inputdata">
            <param name="input_type" type="select" label="Select input dataset options" help="specific dataset input for reading">
                <option value="with_header" selected="true">Dataset with header</option>
                <option value="with_rownames">Dataset with row names</option>
                <option value="with_header_rownames">Dataset with header and row names</option>
                <option value="no_header_rownames">Dataset without header or row names</option>
            </param>
            <when value="with_header">
                <param name="header" type="hidden" value="TRUE"/>
                <param name="row_names_index" type="hidden" value="0"/>
                <param name="sample_name_orientation" type="select" display="radio" multiple="false" label="Sample names orientation" help="Default horizontal: header names are interpreted as sample names">
                    <option value="TRUE" selected="true">horizontal</option>
                    <option value="FALSE">vertial</option>
                </param>
            </when>
            <when value="with_rownames">
                <param name="header" type="hidden" value="FALSE"/>
                <param name="row_names_index" type="data_column" data_ref="input1" label="Select column, for row names" help="WARNING: please consider that using row names might shift the grouping columns"/>
                <param name="sample_name_orientation" type="select" display="radio" label="Sample names orientation" help="default vertial: row names are interpreted as sample names">
                    <option value="TRUE">horizontal</option>
                    <option value="FALSE" selected="true">vertial</option>
                </param>
            </when>
            <when value="with_header_rownames">
                <param name="header" type="hidden" value="TRUE"/>
                <param name="row_names_index" type="data_column" data_ref="input1" label="Select column, for row names" help="WARNING: please consider that using row names might shift the grouping columns"/>
                <param name="sample_name_orientation" type="select" label="Sample names orientation" display="radio" multiple="false" help="deside whether header names or row names are interpreted as sample names">
                    <option value="TRUE" selected="true">horizontal</option>
                    <option value="FALSE">vertial</option>
                </param>
            </when>
            <when value="no_header_rownames">
                <param name="header" type="hidden" value="FALSE"/>
                <param name="row_names_index" type="hidden" value="0"/>
                <param name="sample_name_orientation" type="hidden" value="TRUE"/>
            </when>
        </conditional>
    </xml>
    <xml name="transform">
        <param name="transform" type="select" label="Data transformation">
            <option value="none">Plot the data as it is</option>
            <option value="log2">Log2(value) transform my data</option>
            <option value="log2plus1">Log2(value+1) transform my data</option>
            <option value="log10">Log10(value) transform my data</option>
            <option value="log10plus1">Log10(value+1) transform my data</option>
        </param>
    </xml>
    <xml name="xy_scaling">
        <conditional name="scaling">
            <param name="plot_scaling" type="select" label="Axis scaling">
                <option value="Automatic" selected="true">Automatic axis scaling</option>
                <option value="Defined">User-defined axis scales</option>
            </param>
            <when value="Automatic"/>
            <when value="Defined">
                <param name="xaxismin" type="float" value="0" label="minimal range of x-axis" />
                <param name="xaxismax" type="float" value="3" label="maximal range of x-axis" />
                <param name="yaxismin" type="float" value="0" label="minimal range of y-axis" />
                <param name="yaxismax" type="float" value="3" label="maximal range of y-axis" />
            </when>
        </conditional>
    </xml>
    <xml name="title">
       <param name="title" type="text" value="" label="Plot title">
            <!--<sanitizer sanitize="false"/> -->
        </param>
    </xml>
    <xml name="xy_lab">
        <param name="xlab" type="text" value="Title of x-axis" label="Label for x axis">
            <sanitizer sanitize="false"/>
        </param>
        <param name="ylab" type="text" value="Title of y-axis" label="Label for y axis">
            <sanitizer sanitize="false"/>
        </param>
    </xml>
    <xml name="legend">
        <param name="legend" type="select" label="Legend options">
            <option value="yes">Include legend on plot</option>
            <option value="no">Hide legend</option>
        </param>
    </xml>
    <xml name="theme">
        <param name="theme" type="select" label="Backgound theme for plot">
            <option value="bw">Black and white</option>
            <option value="Default">Default (grey)</option>
        </param>
    </xml>
    <xml name="dimensions">
        <param name="unit_output_dim" type="select" label="Unit of output dimensions" help="Default: inches.">
            <option value="in" selected="true">Inches (in)</option>
            <option value="cm">Centimeters (cm)</option>
            <option value="mm">Millimeters (mm)</option>
        </param>
        <param name="width_output_dim" type="float" value="7" label="width of output"/>
        <param name="height_output_dim" type="float" value="7" label="height of output"/>
        <param name="dpi_output_dim" type="float" value="300" label="dpi of output" help="Plot resolution. Applies only to raster output types."/>
        <param name="additional_output_format" type="select" label="Additional output format" help="PNG is always selected as output format.">
            <option value="none" selected="true">Only PNG</option>
            <option value="pdf">PDF</option>
            <option value="svg">SVG</option>
            <option value="eps">EPS</option>
            <option value="ps">PS</option>
            <option value="tex">TEX (pictex)</option>
            <option value="jpeg">JPEG</option>
            <option value="tiff">TIFF</option>
            <option value="bmp">BMP</option>
        </param>
    </xml>
    <xml name="citations">
        <citations>
            <citation type="bibtex">@book{wickham2009ggplot2,
                author = {Hadley Wickham},
                title = {ggplot2: Elegant Graphics for Data Analysis},
                publisher = {Springer-Verlag New York},
                year = {2009},
                isbn = {978-0-387-98140-6},
                url = {https://ggplot2.tidyverse.org/},
                }
            </citation>
            <yield />
        </citations>
    </xml>
    <xml name="axis_customization" token_label="Axis title options">
        <param name="axis_customization" type="select" label="@LABEL@">
            <option value="default" selected="true">Default</option>
            <option value="defined">User defined label options</option>
        </param>
        <when value="default"/>
        <when value="defined">
            <param name="size" type="float" value="12" label="Axis label size (default = 12)"/>
            <param name="color" type="select" label="Color of axis label">
                <option value="black">Black (default)</option>
                <option value="red">Red</option>
                <option value="white">White</option>
                <option value="blue">Blue</option>
                <option value="orange">Orange</option>
                <option value="yellow">Yellow</option>
                <option value="green">Green</option>
                <option value="purple">Purple</option>
                <option value="magenta">Magenta</option>
                <option value="cyan">Cyan</option>
                <option value="grey">Grey</option>
                <option value="gold">Gold</option>
            </param>
            <param name="face" type="select" label="Font effect of axis label">
                <option value="plain">Normal (default)</option>
                <option value="bold">Bold</option>
                <option value="italic">Italic</option>
            </param>
        </when>
    </xml>
    <xml name="colors">
        <param name="colors" type="select" label="Color schemes to differentiate your groups" >
            <option value="Default">Default color scheme</option>
            <option value="YlOrRd">Yellow to orange to red (discrete, max=9 colors)</option>
            <option value="YlOrBr">Yellow to orange to brown (discrete, max=9 colors)</option>
            <option value="YlGnBu">Yellow to green to blue (discrete, max=9 colors)</option>
            <option value="YlGn">Yellow to green (discrete, max=9 colors)</option>
            <option value="Reds">Shades of red from light to dark (discrete, max=9 colors)</option>
            <option value="RdPu">Red to purple (discrete, max=9 colors)</option>
            <option value="Purples">Shades of purple from light to dark (discrete, max=9 colors)</option>
            <option value="PuRd">Purple to red (discrete, max=9 colors)</option>
            <option value="PuBuGn">Purple to blue to green (discrete, max=9 colors)</option>
            <option value="PuBu">Purple to blue(discrete, max=9 colors)</option>
            <option value="OrRd">Orange to red (discrete, max=9 colors)</option>
            <option value="Oranges">Shades of orange from light to dark (discrete, max=9 colors)</option>
            <option value="Greys">Shades of grey from light to dark (discrete, max=9 colors)</option>
            <option value="Greens">Shades of greens from light to dark (discrete, max=9 colors)</option>
            <option value="GnBu">Green to blue (discrete, max=9 colors)</option>
            <option value="BuPu">Blue to purple (discrete, max=9 colors)</option>
            <option value="BuGn">Blue to green (discrete, max=9 colors)</option>
            <option value="Blues">Shades of blue from light to dark (discrete, max=9 colors)</option>
            <option value="Set1">Set 1 - predefined color pallete (discrete, max=9 colors)</option>
            <option value="Set2">Set 2 - predefined color pallete (discrete, max=8 colors)</option>
            <option value="Set3">Set 3 - predefined color pallete (discrete, max=12 colors)</option>
            <option value="Pastel1">Pastel 1 - predefined pastel color pallete (discrete, max=9 colors)</option>
            <option value="Pastel2">Pastel 2 - predefined pastel color pallete (discrete, max=8 colors)</option>
            <option value="Paired">Paired - predefined color pallete (discrete, max=12 colors)</option>
            <option value="Dark2">Dark 2 - predefined color pallete (discrete, max=12 colors)</option>
            <option value="Accent">Accent - predefined color pallete (discrete, max=12 colors)</option>
            <option value="Spectral">Spectral - Red to yellow to purple (discrete, max=11 colors)</option>
            <option value="RdYlGn">Red to yellow to green (discrete, max=11 colors)</option>
            <option value="RdYlBu">Red to yellow to blue (discrete, max=11 colors)</option>
            <option value="RdGy">Red to grey (discrete, max=11 colors)</option>
            <option value="RdBu">Red to blue (discrete, max=11 colors)</option>
            <option value="PuOr">Purple to orange (discrete, max=11 colors)</option>
            <option value="PRGn">Purple to green (discrete, max=11 colors)</option>
            <option value="BrBG">Brown to teal (discrete, max=11 colors)</option>
        </param>
    </xml>
    <xml name="additional_output">
        <data name="output1" format="png" label="${tool.name} on ${on_string}: png"/>
        <data format="pdf" name="output2" label="${tool.name} on ${on_string}: ${out.additional_output_format}">
            <change_format>
                <when input="out.additional_output_format" value="svg" format="svg" />
                <when input="out.additional_output_format" value="eps" format="eps" />
                <when input="out.additional_output_format" value="ps" format="ps" />
                <when input="out.additional_output_format" value="tex" format="txt" />
                <when input="out.additional_output_format" value="jpeg" format="jpg" />
                <when input="out.additional_output_format" value="tiff" format="tiff" />
                <when input="out.additional_output_format" value="bmp" format="bmp" />
            </change_format>
            <filter>out['additional_output_format'] != "none"</filter>
        </data>
    </xml>
    <xml name="points_options">
        <conditional name="points">
            <param name="pointoptions" type="select" label="Data point options">
                <option value="default" selected="true">Default</option>
                <option value="defined">User defined point options</option>
            </param>
            <when value="default">
                <!--Do nothing here -->
            </when>
            <when value="defined">
                <param name="size" type="float" value="1" label="relative size of points" />
                <param name="alpha" type="float" value="1" label="Transparency of points (On a scale of 0-1; 0=transparent, 1=default)" />
                <param name="pointcolor" type="select" label="Color of data points" >
                    <option value="black">Black (default)</option>
                    <option value="red">Red</option>
                    <option value="white">White</option>
                    <option value="blue">Blue</option>
                    <option value="orange">Orange</option>
                    <option value="yellow">Yellow</option>
                    <option value="green">Green</option>
                    <option value="purple">Purple</option>
                    <option value="magenta">Magenta</option>
                    <option value="cyan">Cyan</option>
                    <option value="grey">Grey</option>
                    <option value="gold">Gold</option>
                </param>
                <param name="shape" type="select" label="Shape of data points" >
                    <option value="0">square</option>
                    <option value="1">circle</option>
                    <option value="2">triangle point up</option>
                    <option value="3">plus</option>
                    <option value="4">cross</option>
                    <option value="5">diamond</option>
                    <option value="6">triangle point down</option>
                    <option value="7">square cross</option>
                    <option value="8">star</option>
                    <option value="9">diamond plus</option>
                    <option value="10">circle plus</option>
                    <option value="11">triangles up and down</option>
                    <option value="12">square plus</option>
                    <option value="13">circle cross</option>
                    <option value="14">square and triangle down</option>
                    <option value="15">filled square</option>
                    <option value="16">filled circle</option>
                    <option value="17">filled triangle point-up</option>
                    <option value="18">filled diamond</option>
                    <option value="19">solid circle</option>
                    <option value="20">bullet (smaller circle)</option>
                </param>
            </when>
        </conditional>
    </xml>
    <xml name="data_input">
        <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"/>
    </xml>

    <xml name="axes_labels">
        <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"/>
    </xml>
    
    <xml name="export_data">
        <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>
</macros>