annotate macros.xml @ 1:cb04f3235a4e draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 97544038b04c02170ab82877db666fa3022e4469

<?xml version="1.0"?>
<macros>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@VERSION@">r-ggplot2</requirement>
            <yield />
        </requirements>
    </xml>
    <token name="@VERSION@">2.2.1</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 $transform == "log2"
    input["value"] <- log2(input["value"])
#elif $transform == "log2plus1"
    input["value"] <- log2(input["value"]+1)
#elif $transform == "log10"
    input["value"] <- log10(input["value"])
#elif $transform == "log10plus1"
    input["value"] <- log10(input["value"]+1)
#end if
    ]]></token>

    <xml name="transform">
        <param name="transform" type="select" label="Advanced - log 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>

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

    <xml name="xy_scaling">
        <conditional name="scaling">
            <param name="plot_scaling" type="select" label="Advanced - Axis scaling">
                <option value="Automatic" selected="True">Automatic axis scaling</option>
                <option value="Defined">User deined axis scales</option>
            </param>
            <when value="Automatic">
                <!--Do nothing here -->
            </when>
            <when value="Defined">
                <param name="xaxismin" type="integer" value="0" label="minimal range of x-axis" />
                <param name="xaxismax" type="integer" value="3" label="maximal range of x-axis" />
                <param name="yaxismin" type="integer" value="0" label="minimal range of y-axis" />
                <param name="yaxismax" type="integer" value="3" label="maximal range of y-axis" />
            </when>
        </conditional>
    </xml>
    <xml name="title">
        <param name="title" type="text" value="plot title" label="Title of plot" />
    </xml>
    <xml name="xy_lab">
        <param name="xlab" type="text" value="title of x-axis" label="Label for x-axis"/>
        <param name="ylab" type="text" value="title of y-axis" label="Label for y-axis"/> 
    </xml>
    <xml name="dimensions">
        <param name="with_output_dim" type="float" value="7" label="width of output" help="in inches" />
        <param name="height_output_dim" type="float" value="7" label="height of output" help="in inches" />
    </xml>
    <xml name="citations">
        <citations>
            <citation type="bibtex">@Book{
                author = {Hadley Wickham},
                title = {ggplot2: Elegant Graphics for Data Analysis},
                publisher = {Springer-Verlag New York},
                year = {2009},
                isbn = {978-0-387-98140-6},
                url = {http://ggplot2.org}
                }
            </citation>
        </citations>
    </xml>

    <xml name="axis_customization" token_label="Advanced - 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">
            <!--Do nothing here -->
        </when>
        <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>

</macros>