# HG changeset patch
# User moheydarian
# Date 1484149528 18000
# Node ID 5a901c0cb006acf356b55253ff85f85ced640cc8
# Parent  b342326db6dd52fea9aec8c83bd26b90f5c781b3
Uploaded

diff -r b342326db6dd -r 5a901c0cb006 ggplot_point.xml
--- a/ggplot_point.xml	Wed Jan 11 10:37:50 2017 -0500
+++ b/ggplot_point.xml	Wed Jan 11 10:45:28 2017 -0500
@@ -7,7 +7,7 @@
         <exit_code range="1:" />
     </stdio>
     <command><![CDATA[
-        Rscript ggplotpointscript.R --input "$input1" --title "$title" 
+        Rscript 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"
@@ -24,6 +24,7 @@
            --colors=irrelevant
            --colororder=1
         #end if
+
         #if str( $points.pointoptions ) == "Defined":
             --size ${points.size}
             --alpha ${points.alpha}
@@ -33,6 +34,7 @@
            --alpha=1
            --pointcolor=black
         #end if
+
         #if str( $scaling.Plot_scaling ) == "Defined":
             --xaxismin=${scaling.xaxismin}
             --xaxismax=${scaling.xaxismax}
@@ -44,6 +46,7 @@
            --yaxismin=2
            --yaxismax=3
         #end if
+
         #if str( $axistitlecustomization.axistitlecust ) == "Defined":
             --axistitlesize ${axistitlecustomization.axistitlesize}
             --axistitlecolor ${axistitlecustomization.axistitlecolor}
@@ -53,6 +56,7 @@
             --axistitlecolor=black
             --axistitleface=plain
         #end if
+
         #if str( $axistextcustomization.axistextcust ) == "Defined":
             --axistextsize ${axistextcustomization.axistextsize}
             --axistextcolor ${axistextcustomization.axistextcolor}
@@ -62,6 +66,7 @@
             --axistextcolor=black
             --axistextface=plain
         #end if
+
         #if str( $plottitlecustomization.plottitlecust ) == "Defined":
             --plottitlesize ${plottitlecustomization.plottitlesize}
             --plottitlecolor ${plottitlecustomization.plottitlecolor}
@@ -71,6 +76,7 @@
             --plottitlecolor=black
             --plottitleface=plain
         #end if
+
         #if str( $dimensions.plotdim ) == "Defined":
             --woutputdim ${dimensions.woutputdim}
             --houtputdim ${dimensions.houtputdim}
@@ -78,6 +84,7 @@
            --woutputdim=7
            --houtputdim=7
         #end if
+
     ]]></command>
     <inputs>
         <param name="input1" type="data" format="tabular" label="Input (tabular format)" />
@@ -356,10 +363,18 @@
     </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>
@@ -372,3 +387,4 @@
     }</citation>
         </citations>
     </tool>      
+