# HG changeset patch
# User rnateam
# Date 1449781337 18000
# Node ID b6263bd3666fdf027adb66b21e0a9d87efd99fcd
# Parent  be094e3b86f597addac4777d616fe11867b1ce27
planemo upload commit 04caebff47f47204ffb886ba194d7885cd0b35e8

diff -r be094e3b86f5 -r b6263bd3666f metilene.xml
--- a/metilene.xml	Thu Dec 10 12:23:28 2015 -0500
+++ b/metilene.xml	Thu Dec 10 16:02:17 2015 -0500
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="utf-8"?>
-<tool id="metilene" name="metilene" version="0.2-4.3">
+<tool id="metilene" name="metilene" version="0.2-4.4">
     <description>
         calling differentially methylated regions from
         bisulfite sequencing data
@@ -9,7 +9,7 @@
         <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="v2.24.0" >bedtools</requirement>
+        <requirement type="package" version="2.24" >bedtools</requirement>
         <requirement type="package" version="0.2-4" >metilene</requirement>
         <requirement type="package" version="8.22">gnu_coreutils</requirement>
     </requirements>
@@ -36,18 +36,18 @@
     -M $Options.opt_M -m $Options.opt_m -d $Options.opt_d -t 1 -f 1 -v $Options.opt_v
     metilene_g1_g2.input
     >$output_bedlike
-    2>$output_stderr
+    2>/dev/null
     ;
     ## =============== postprocessing
-    cut -f1-4 $output_bedlike > $output_bedgraph
+    cut -f1-4 $output_bedlike > $output_bedgraph 2>/dev/null
     ;
     ## write to job directory ...
     metilene_output.pl -q $output_bedlike -p 0.05 -o ./metilene >/dev/null 2>/dev/null
     ;
     ## ... and move to output files
-    mv metilene_qval.0.05.bedgraph $output_qval_bedgraph ;
-    mv metilene_qval.0.05.out $output_qval_out ;
-    mv metilene_qval.0.05.pdf $output_qval_pdf
+    mv metilene_qval.0.05.bedgraph $output_qval_bedgraph 2>/dev/null;
+    mv metilene_qval.0.05.out $output_qval_out 2>/dev/null;
+    mv metilene_qval.0.05.pdf $output_qval_pdf 2>/dev/null
     ]]></command>
     
     <inputs>
@@ -111,8 +111,6 @@
               label="${tool.name} on ${on_string}" />
         <data format="bedgraph" name="output_bedgraph" 
               label="${tool.name} on ${on_string}" />
-        <data format="txt" name="output_stderr" 
-              label="${tool.name} stderr ouptut on ${on_string}" />
         <data format="bedgraph" name="output_qval_bedgraph" 
               label="${tool.name} qval&lt;0.05 bedgraph on ${on_string}" />
         <data format="pdf" name="output_qval_pdf" 
diff -r be094e3b86f5 -r b6263bd3666f tool_dependencies.xml
--- a/tool_dependencies.xml	Thu Dec 10 12:23:28 2015 -0500
+++ b/tool_dependencies.xml	Thu Dec 10 16:02:17 2015 -0500
@@ -46,6 +46,10 @@
                   <source>metilene_output.pl</source>
                   <destination>$INSTALL_DIR/bin</destination>
               </action>
+              <action type="move_file">
+                  <source>metilene_output.R</source>
+                  <destination>$INSTALL_DIR/bin</destination>
+              </action>
 
               <!-- include installation bin directory in path -->
               <action type="set_environment">