# HG changeset patch
# User mvdbeek
# Date 1473871376 14400
# Node ID b4102b1634885f919b00744d09777aae0ec18212
# Parent  11627baf830ef793858277a2169ca5fadb0349d2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit 1b68ca3d083c5879e996a9df5e22963dfc9c3f90-dirty

diff -r 11627baf830e -r b4102b163488 scatterplot.py
--- a/scatterplot.py	Wed Sep 14 12:40:20 2016 -0400
+++ b/scatterplot.py	Wed Sep 14 12:42:56 2016 -0400
@@ -4,7 +4,12 @@
 import sys
 
 from numpy import array
-from rpy import r
+import rpy2.rpy_classic as rpy
+from rpy2.robjects.numpy2ri import numpy2ri
+
+
+rpy.set_default_mode(rpy.NO_CONVERSION)
+r = rpy.r
 
 
 def stop_err(msg):
@@ -65,8 +70,9 @@
 
     if skipped_lines < i:
         try:
+            a = numpy2ri(array( matrix ))
             r.pdf( out_fname, 8, 8 )
-            r.plot( array( matrix ), type="p", main=title, xlab=xlab, ylab=ylab, col="blue", pch=19 )
+            r.plot( a, type="p", main=title, xlab=xlab, ylab=ylab, col="blue", pch=19 )
             r.dev_off()
         except Exception, exc:
             stop_err( "%s" % str( exc ) )
@@ -77,7 +83,5 @@
     if skipped_lines > 0:
         print "Skipped %d lines starting with line #%d, value '%s' in column %d is not numeric." % ( skipped_lines, first_invalid_line, invalid_value, invalid_column )
 
-    r.quit( save="no" )
-
 if __name__ == "__main__":
     main()
diff -r 11627baf830e -r b4102b163488 scatterplot.xml
--- a/scatterplot.xml	Wed Sep 14 12:40:20 2016 -0400
+++ b/scatterplot.xml	Wed Sep 14 12:42:56 2016 -0400
@@ -1,8 +1,8 @@
-<tool id="scatterplot_rpy" name="Scatterplot" version="1.0.1">
+<tool id="scatterplot_rpy" name="Scatterplot" version="1.0.2">
   <description>of two numeric columns</description>
   <requirements>
     <requirement type="package" version="1.9">numpy</requirement>
-    <requirement type="package" version="1.0.3">rpy</requirement>
+    <requirement type="package" version="2.7.8">rpy2</requirement>
   </requirements>
   <command interpreter="python">scatterplot.py $input $out_file1 $col1 $col2 "$title" "$xlab" "$ylab"</command>
   <inputs>
@@ -16,8 +16,6 @@
   <outputs>
     <data format="pdf" name="out_file1" />
   </outputs>
-  <!-- TODO: uncomment the following test when we have tools.update_state() working for 
-       multiple dependents with the same dependency.
   <tests>
     <test>
       <param name="input" value="scatterplot_in1.tabular" ftype="tabular"/>
@@ -26,10 +24,9 @@
       <param name="title" value="Scatterplot"/>
       <param name="xlab" value="V1"/>
       <param name="ylab" value="V2"/>
-      <output name="out_file1" file="scatterplot_out1.pdf" />
+      <output name="out_file1" file="scatterplot_out1.pdf" compare="sim_size" />
     </test>
   </tests>
-  -->
   <help>
 .. class:: infomark
 
diff -r 11627baf830e -r b4102b163488 tool_dependencies.xml
--- a/tool_dependencies.xml	Wed Sep 14 12:40:20 2016 -0400
+++ b/tool_dependencies.xml	Wed Sep 14 12:42:56 2016 -0400
@@ -3,7 +3,7 @@
     <package name="numpy" version="1.9">
         <repository changeset_revision="1e2b7e63dec2" name="package_numpy_1_9" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
-    <package name="rpy" version="1.0.3">
-        <repository changeset_revision="3e11ba53f2a6" name="package_rpy_1_0_3" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    <package name="rpy2" version="2.7.8">
+        <repository changeset_revision="93507635aa0b" name="package_rpy2_2_7_8" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>