# HG changeset patch
# User devteam
# Date 1473932211 14400
# Node ID 1dacc8aeb4526d75cd8fa3b17b685c8950a8a476
# Parent  53eb2c4127830e5c766289e24846c3c8505ec776
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit 93df3895fbf2fa44ff279303093fb89b79081687

diff -r 53eb2c412783 -r 1dacc8aeb452 scatterplot.py
--- a/scatterplot.py	Fri Dec 18 19:14:12 2015 -0500
+++ b/scatterplot.py	Thu Sep 15 05:36:51 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 53eb2c412783 -r 1dacc8aeb452 scatterplot.xml
--- a/scatterplot.xml	Fri Dec 18 19:14:12 2015 -0500
+++ b/scatterplot.xml	Thu Sep 15 05:36:51 2016 -0400
@@ -1,8 +1,10 @@
-<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>
+    <!-- explicit R requirement is necessary for toolshed package, conda rpy2 comes with R -->
+    <requirement type="package" version="3.2.1">R</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 +18,6 @@
   <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 +26,9 @@
       <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 53eb2c412783 -r 1dacc8aeb452 tool_dependencies.xml
--- a/tool_dependencies.xml	Fri Dec 18 19:14:12 2015 -0500
+++ b/tool_dependencies.xml	Thu Sep 15 05:36:51 2016 -0400
@@ -1,9 +1,12 @@
 <?xml version="1.0"?>
 <tool_dependency>
     <package name="numpy" version="1.9">
-        <repository changeset_revision="f9289486f06d" name="package_numpy_1_9" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="5f2b261ffc5b" name="package_python_2_7_numpy_1_9" owner="iuc" 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="R" version="3.2.1">
+        <repository changeset_revision="77d439695328" name="package_r_3_2_1" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="rpy2" version="2.7.8">
+        <repository changeset_revision="335987b7d119" name="package_rpy2_2_7_8" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>