# HG changeset patch
# User devteam
# Date 1421954727 18000
# Node ID d917c1473e8e1a6f0463801f1eda97271c2603d9
# Parent  88ecf2b559a046f5d99ed5d468d793290990b54c
Uploaded

diff -r 88ecf2b559a0 -r d917c1473e8e karyotype/karyotype_plot.xml
--- a/karyotype/karyotype_plot.xml	Thu Jan 22 14:06:47 2015 -0500
+++ b/karyotype/karyotype_plot.xml	Thu Jan 22 14:25:27 2015 -0500
@@ -1,6 +1,6 @@
 <tool id="karyotype_Plot_1" name="Karyotype Plotting tool" version="1.0.0">
   <description>for multiple series </description>
-  <command interpreter="bash">r_wrapper.sh $script_file</command>
+  <command interpreter="bash">r_wrapper.sh \$R_SCRIPT_PATH/$script_file</command>
 
   <inputs>
     <param name="main" type="text" value="" size="30" label="Plot Title"/>
@@ -149,6 +149,7 @@
   <requirements>
     	<requirement type="set_environment">R_SCRIPT_PATH</requirement>
     	<requirement type="package" version="2.15.0">R</requirement>
+    	<requirement type="package" version="3.4.1">gtools</requirement>
   </requirements>
 	
 <help>
diff -r 88ecf2b559a0 -r d917c1473e8e karyotype/r_wrapper.sh
diff -r 88ecf2b559a0 -r d917c1473e8e karyotype/tool_dependencies.xml
--- a/karyotype/tool_dependencies.xml	Thu Jan 22 14:06:47 2015 -0500
+++ b/karyotype/tool_dependencies.xml	Thu Jan 22 14:25:27 2015 -0500
@@ -6,4 +6,16 @@
     <package name="R" version="2.15.0">
         <repository changeset_revision="6c34eaa82fed" name="package_r_2_15_0" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
+    <package name="gtools" version="3.4.1">
+        <install version="1.0">
+            <actions>
+                <action type="setup_r_environment">
+                    <repository changeset_revision="6c34eaa82fed" name="package_r_2_15_0" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu">
+                        <package name="R" version="2.15.0" />
+                    </repository>
+                    <package>https://depot.galaxyproject.org/package/noarch/gtools_3.4.1.tar.gz</package>
+                </action>
+            </actions>
+        </install>
+    </package>
 </tool_dependency>