# HG changeset patch
# User rnateam
# Date 1449768154 18000
# Node ID f827043c2a970552280d2ef609ad9b9aae50d5ce
# Parent  91132980aecc37e3a25ba21e4810389e7b141c7d
planemo upload commit f14004d917b2be0c2f8678f14f069b1fd4ffa1a9-dirty

diff -r 91132980aecc -r f827043c2a97 metilene.xml
--- a/metilene.xml	Thu Dec 10 11:49:29 2015 -0500
+++ b/metilene.xml	Thu Dec 10 12:22:34 2015 -0500
@@ -1,16 +1,17 @@
 <?xml version="1.0" encoding="utf-8"?>
-<tool id="metilene" name="metilene" version="0.2-4.2">
+<tool id="metilene" name="metilene" version="0.2-4.3">
     <description>
         calling differentially methylated regions from
         bisulfite sequencing data
     </description>
     
     <requirements>
-        <requirement type="package" version="5.18" >perl</requirement>
+        <requirement type="binary">Rscript</requirement>
+        <requirement type="package" version="5.18.1" >perl</requirement>
         <requirement type="package" version="3.2.1" >R</requirement>
-        <requirement type="package" version="3.2.1" >R-ggplot2</requirement>
         <requirement type="package" version="v2.24.0" >bedtools</requirement>
         <requirement type="package" version="0.2-4" >metilene</requirement>
+        <requirement type="package" version="8.22">gnu_coreutils</requirement>
     </requirements>
     
     <stdio>
diff -r 91132980aecc -r f827043c2a97 tool_dependencies.xml
--- a/tool_dependencies.xml	Thu Dec 10 11:49:29 2015 -0500
+++ b/tool_dependencies.xml	Thu Dec 10 12:22:34 2015 -0500
@@ -1,13 +1,32 @@
 <?xml version="1.0"?>
 <tool_dependency>
+    <package name="perl" version="5.18.1">
+        <repository changeset_revision="2590d4683481" name="package_perl_5_18" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="R" version="3.2.1">
+        <repository changeset_revision="c6ebd3a51334" name="package_r_3_2_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="bedtools" version="2.24">
+        <repository changeset_revision="e6f4a7398a47" name="package_bedtools_2_24" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="gnu_coreutils" version="8.22">
+        <repository changeset_revision="1016a386a647" name="package_gnu_coreutils_8_22" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    </package>
+
     <package name="metilene" version="0.2-4">
         <install version="1.0">
             <actions>
+
+               <action type="setup_r_environment">
+                   <repository changeset_revision="c6ebd3a51334" name="package_r_3_2_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
+                       <package name="R" version="3.2.1" />
+                   </repository>
+                   <package>https://github.com/bgruening/download_store/raw/master/blockclust/r-packages/ggplot2_0.9.3.1.tar.gz</package>
+               </action>
+ 
+
               <!-- don't use download_by_url, since archive name != directory name --> 
-              <action type="download_file">
-		http://www.bioinf.uni-leipzig.de/Software/metilene/metilene_v02-4.tar.gz
-	      </action>
-              
+              <action type="download_file">http://www.bioinf.uni-leipzig.de/Software/metilene/metilene_v02-4.tar.gz</action>
               <action type="shell_command">tar xfz metilene_v02-4.tar.gz</action>
               
               <action type="change_directory">metilene_v0.2-4</action>
@@ -30,8 +49,8 @@
 
               <!-- include installation bin directory in path -->
               <action type="set_environment">
-                <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
-		<environment_variable name="METILENE_ROOT_PATH" action="set_to">$INSTALL_DIR</environment_variable>
+                <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
+		<environment_variable action="set_to" name="METILENE_ROOT_PATH">$INSTALL_DIR</environment_variable>
               </action>
             </actions>
         </install>