# HG changeset patch
# User moheydarian
# Date 1480713117 18000
# Node ID c48e66dcb9c4b5ba15d97a284a8b0d919b584f80
# Parent  37e17dfc9add60418ecfaeec9de205adf5478a50
Uploaded

diff -r 37e17dfc9add -r c48e66dcb9c4 ggplot_point_8.10.2.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ggplot_point_8.10.2.xml	Fri Dec 02 16:11:57 2016 -0500
@@ -0,0 +1,389 @@
+<tool id="ggplot_point_8.10.2" name="Scatterplot w ggplot2 to pdf 8.10.2" 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 ggplotscript8.10.2.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>