Mercurial > repos > moheydarian > ggplot_scatterplot
changeset 0:d0564619e245 draft
Uploaded
| author | moheydarian |
|---|---|
| date | Fri, 02 Dec 2016 15:33:31 -0500 |
| parents | |
| children | 37e17dfc9add |
| files | ggplot_point.xml |
| diffstat | 1 files changed, 389 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ggplot_point.xml Fri Dec 02 15:33:31 2016 -0500 @@ -0,0 +1,389 @@ +<tool id="ggplot_point" name="Scatterplot with ggplott" version="0.1.2"> + <requirements> + <requirement type="package">getopt</requirement> + <requirement type="package">ggplot2</requirement> + </requirements> + <stdio> + <exit_code range="1:" /> + </stdio> + <command><![CDATA[ + Rscript /Users/cmdb/Downloads/Galaxy-wrapper-for-ggplot2-scatterplot-master/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>