ggplot_point.xml

<tool id="ggplot_point" name="Scatterplot w ggplot2" version="0.1.3">
    <requirements>
        <requirement type="package">r-getopt</requirement>
        <requirement type="package">r-ggplot2</requirement>
    </requirements>
    <stdio>
        <exit_code range="1:" />
    </stdio>
    <command><![CDATA[
        Rscript '${__tool_directory__}/ggplotpointscript.R' --input "$input1" --title "$title" 
        --theme "${theme.theme_selector}" --xplot "$xplot" --yplot "$yplot" --scaling "$scaling.Plot_scaling" --points "$points.pointoptions" --dim "$dimensions.plotdim" --factor "$factor.factoring" --transform "$transformation.transform" --xlab "$xlab" --ylab "$ylab" 
        --axistitlecust "$axistitlecustomization.axistitlecust" --axistextcust "$axistextcustomization.axistextcust" 
        --plottitlecust "$plottitlecustomization.plottitlecust" --gridlinecust "$gridlinecustomization.gridlinecust" --output "Rplot.pdf"
        #if str( $factor.factoring ) == "Single":
            --factorcol ${factor.factorcol}
            --colors ${factor.colors}
            --colororder ${factor.colororder}
        #elif str( $factor.factoring ) == "Multiple":
            --factorcol ${factor.factorcol}
            --colors=irrelevant
            --colororder=1
        #else:
           --factorcol=1
           --colors=irrelevant
           --colororder=1
        #end if

        #if str( $points.pointoptions ) == "Defined":
            --size ${points.size}
            --alpha ${points.alpha}
            --pointcolor ${points.pointcolor}
        #else:
           --size=1
           --alpha=1
           --pointcolor=black
        #end if

        #if str( $scaling.Plot_scaling ) == "Defined":
            --xaxismin=${scaling.xaxismin}
            --xaxismax=${scaling.xaxismax}
            --yaxismin=${scaling.yaxismin}
            --yaxismax=${scaling.yaxismax}
        #else:
           --xaxismin=0
           --xaxismax=1
           --yaxismin=2
           --yaxismax=3
        #end if

        #if str( $axistitlecustomization.axistitlecust ) == "Defined":
            --axistitlesize ${axistitlecustomization.axistitlesize}
            --axistitlecolor ${axistitlecustomization.axistitlecolor}
            --axistitleface ${axistitlecustomization.axistitleface}
        #else:
            --axistitlesize=12
            --axistitlecolor=black
            --axistitleface=plain
        #end if

        #if str( $axistextcustomization.axistextcust ) == "Defined":
            --axistextsize ${axistextcustomization.axistextsize}
            --axistextcolor ${axistextcustomization.axistextcolor}
            --axistextface ${axistextcustomization.axistextface}
        #else:
            --axistextsize=12
            --axistextcolor=black
            --axistextface=plain
        #end if

        #if str( $plottitlecustomization.plottitlecust ) == "Defined":
            --plottitlesize ${plottitlecustomization.plottitlesize}
            --plottitlecolor ${plottitlecustomization.plottitlecolor}
            --plottitleface ${plottitlecustomization.plottitleface}
        #else:
            --plottitlesize=12
            --plottitlecolor=black
            --plottitleface=plain
        #end if

        #if str( $dimensions.plotdim ) == "Defined":
            --woutputdim ${dimensions.woutputdim}
            --houtputdim ${dimensions.houtputdim}
        #else:
           --woutputdim=7
           --houtputdim=7
        #end if

    ]]></command>
    <inputs>
        <param name="input1" type="data" format="tabular" label="Input (tabular format)" />
        <param name="xplot" type="integer" value="8" label="Column to plot on x-axis" />
        <param name="yplot" type="integer" value="9" label="Column to plot on y-axis" />
        <param name="title" size="30" type="text" value="plot title" label="Title of plot" />
        <param name="xlab" size="30" type="text" value="title of x-axis" label="Label for x-axis"/>
        <param name="ylab" size="30" type="text" value="title of y-axis" label="Label for y-axis"/> 
        <conditional name="points">
            <param name="pointoptions" type="select" label="Advanced - 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" size="4" type="float" value="1" label="relative size of points" />
                <param name="alpha" size="4" 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>
            </when>
        </conditional>
        <conditional name="factor">
            <param name="factoring" type="select" label="Advanced - plotting multiple groups" >
                <option value="Default" selected="True">No thanks - just plot the data as one group</option>
                <option value="Single">Plot multiple groups of data on one plot</option>
                <option value="Multiple">Plot multiple groups of data on individual plots</option>
            </param>
            <when value="Default">
                <!--Do nothing here -->
            </when>
            <when value="Single">
                <param name="factorcol" size="4" type="integer" value="1" label="column differentiating the different groups" />
                <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>
                <param name="colororder" type="select" label="Reverse color scheme" >
                    <option value="1">Default order of color scheme</option>
                    <option value="-1">Reverse the order of my color scheme</option>
                </param> 
            </when>
            <when value="Multiple">
                <param name="factorcol" size="4" type="integer" value="1" label="column differentiating the different groups" />
            </when>
        </conditional>
        <conditional name="transformation">
            <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>
             <when value="none">
                <!--Do nothing here -->
            </when>
             <when value="log2">
                <!--Do nothing here -->
            </when>
             <when value="log2plus1">
                <!--Do nothing here -->
            </when>
             <when value="log10">
                <!--Do nothing here -->
            </when>
             <when value="log10plus1">
                <!--Do nothing here -->
            </when>
        </conditional>
        <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 defined axis scales</option>
            </param>
            <when value="Automatic">
                <!--Do nothing here -->
            </when>
            <when value="Defined">
                <param name="xaxismin" size="4" type="integer" value="0" label="minimal range of x-axis" />
                <param name="xaxismax" size="4" type="integer" value="3" label="maximal range of x-axis" />
                <param name="yaxismin" size="4" type="integer" value="0" label="minimal range of y-axis" />
                <param name="yaxismax" size="4" type="integer" value="3" label="maximal range of y-axis" />
            </when>
        </conditional>
        <conditional name="theme">
            <param name="theme_selector" type="select" label="Advanced - backgound theme for plot">
              <option value="bw">Black and white</option>
              <option value="Default">Default (grey)</option>
            </param>
            <when value="bw"/>
            <when value="Default"></when>
        </conditional>
        <conditional name="axistitlecustomization">
            <param name="axistitlecust" type="select" label="Advanced - axis label options">
                <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="axistitlesize" size="4" type="float" value="12" label="Axis label size (default = 12)"/>
                <param name="axistitlecolor" 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="axistitleface" size="4" 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>
        </conditional>
        <conditional name="axistextcustomization">
            <param name="axistextcust" type="select" label="Advanced - axis text options">
                <option value="Default" selected="True">Default</option>
                <option value="Defined">User defined axis text options</option>
            </param>
            <when value="Default">
                <!--Do nothing here -->
            </when>
            <when value="Defined">
                <param name="axistextsize" size="4" type="float" value="12" label="Axis text size (default = 12)"/>
                <param name="axistextcolor" type="select" label="Color of axis text">
                    <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="axistextface" size="4" type="select" label="Font effect of axis text">
                    <option value="plain">Normal (default)</option>
                    <option value="bold">Bold</option>
                    <option value="italic">Italic</option>
                </param>    
            </when>
        </conditional>
        <conditional name="plottitlecustomization">
            <param name="plottitlecust" type="select" label="Advanced - Plot title options">
                <option value="Default" selected="True">Default</option>
                <option value="Defined">User defined plot title options</option>
            </param>
            <when value="Default">
                <!--Do nothing here -->
            </when>
            <when value="Defined">
                <param name="plottitlesize" size="4" type="float" value="12" label="Plot title size (default = 12)"/>
                <param name="plottitlecolor" type="select" label="Color of plot title">
                    <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="plottitleface" size="4" type="select" label="Font effect of plot title">
                    <option value="plain">Normal (default)</option>
                    <option value="bold">Bold</option>
                    <option value="italic">Italic</option>
                </param>    
            </when>
        </conditional>
        <conditional name="gridlinecustomization">
            <param name="gridlinecust" type="select" label="Advanced - grid lines">
              <option value="Default">Default grid lines</option>
              <option value="hidemajor">Hide major grid lines</option>
              <option value="hideminor">Hide minor grid lines</option>
              <option value="hideboth">Hide major and minor grid lines</option>
            </param>
             <when value="Default">
                <!--Do nothing here -->
            </when>
             <when value="hidemajor">
                <!--Do nothing here -->
            </when>
             <when value="hideminor">
                <!--Do nothing here -->
            </when>
             <when value="hideboth">
                <!--Do nothing here -->
            </when>
        </conditional>
        <conditional name="dimensions">
            <param name="plotdim" type="select" label="Advanced - output dimensions">
                <option value="Default" selected="True">Default</option>
                <option value="Defined">User defined output dimensions</option>
            </param>
            <when value="Default">
                <!--Do nothing here -->
            </when>
            <when value="Defined">
                <param name="woutputdim" size="4" type="float" value="7" label="width of output (inches)" />
                <param name="houtputdim" size="4" type="float" value="7" label="height of output (inches)" />
            </when>
        </conditional>
    </inputs>
    <outputs>
        <!-- <data name="output1" format="png" from_work_dir="Rplot.png"/> -->
        <data name="output1" format="pdf" from_work_dir="Rplot.pdf"/>
    </outputs>
    <tests>
        <test>
            <param name="input1" value="input.txt"/>
            <output name="output1" file="Rplot.pdf"/>
        </test>
    </tests>
    <help><![CDATA[
        This tool will generate a scatterplot representing data from two groups/conditions. 

        The input data should be in tabular format and the user can determine which groups (columns) to plot.

        Multiple groups can be plotted on the same or multiple plots by providing a column with a group identifier under "Advanced - plotting multiple groups".

        Feel free to explore the (many) advanced options to customize your plot. Galaxy makes this type optimization easy for the user!  

        The ouput is a pdf file with your scatterplot. The dimensions of this file can be modified under "Advanced - output dimensions"




        Please report issues at: https://github.com/MoHeydarian/Galaxy-wrapper-for-ggplot2-scatterplot
    ]]></help>
     <citations>
        <citation type="bibtex">
    @misc{renameTODO,
      author = {8.5.2016, FirstTODO},
      year = {TODO},
      title = {TODO},
      url = {http://docs.ggplot2.org/current/geom_point.html},
    }</citation>
        </citations>
    </tool>