# HG changeset patch
# User rnateam
# Date 1468409931 14400
# Node ID af2c31467ca05c7b863e30e144bb4db583e7c16d
# Parent  48462181c62865d5eebe63bab10c76329e07153c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/metilene commit 0dc67759bcbdf5a8a285ded9ba751340d741fe63

diff -r 48462181c628 -r af2c31467ca0 metilene.xml
--- a/metilene.xml	Tue Feb 23 07:27:45 2016 -0500
+++ b/metilene.xml	Wed Jul 13 07:38:51 2016 -0400
@@ -1,12 +1,15 @@
 <?xml version="1.0" encoding="utf-8"?>
-<tool id="metilene" name="metilene" version="0.2-4.1">
+<tool id="metilene" name="metilene" version="0.2.6.0">
     <description>
         calling differentially methylated regions from bisulfite sequencing data
     </description>
     <requirements>
-        <requirement type="package" version="0.2-4">metilene</requirement>
+        <requirement type="package" version="0.2.6">metilene</requirement>
         <requirement type="package" version="5.18.1">perl</requirement>
-        <requirement type="package" version="0.9.3">r_ggplot2</requirement>
+        <!--requirement type="package" version="3.2.1">R</requirement-->
+        <!--requirement type="package" version="0.9.3">r_ggplot2</requirement-->
+
+        <requirement type="package" version="2.0.0">r-ggplot2</requirement>
         <requirement type="package" version="2.24">bedtools</requirement>
         <requirement type="package" version="8.22">gnu_coreutils</requirement>
     </requirements>
@@ -14,31 +17,39 @@
         <exit_code range=":-1"/>
         <exit_code range="1:" />
     </stdio>
-    <version_command>echo "0.2-4"</version_command>
+    <version_command>echo "0.2.6"</version_command>
     <command><![CDATA[
     ## preprocessing
     ## generate metilene_g1_g2.input from multiple bedgraph files
     metilene_input.pl
         --in1 "$opt_in1"
         --in2 "$opt_in2"
-        >/dev/null 2>/dev/null
+        >/dev/null 
+       ##2>/dev/null
     &&
     ## metilene main program
     metilene
         -M $Options.opt_M
         -m $Options.opt_m
         -d $Options.opt_d
-        -t 1
+        -t \${GALAXY_SLOTS:-4}
         #if $B:
             -f 2
             -B "$B"
         #else:
             -f 1
         #end if
+        #if $Options.Y:
+	   -Y $Options.Y
+        #end if
+        #if $Options.X:
+           -X $Options.X
+        #end if
+
         -v $Options.opt_v
         metilene_g1_g2.input
         > $output_bedlike
-        2> /dev/null
+        ##2> /dev/null
     &&
     ## postprocessing
     cut -f1-4 $output_bedlike > $output_bedgraph 2>/dev/null
@@ -47,7 +58,9 @@
     metilene_output.pl
         -q $output_bedlike
         -p 0.05
-        -o ./metilene >/dev/null 2>/dev/null
+        -o ./metilene 
+        ##>/dev/null 
+        ##2>/dev/null
     ]]></command>
     <inputs>
         <!-- input bedgraph files 1 -->
@@ -73,6 +86,14 @@
                 label="The minimum # of CpGs in a DMR"
                 help="-m, --mincpgs"/>
 
+            <param argument="X" type="integer" value="" optional="True"
+                label="Specify how many replicates must contain data for a certain CpG position in group 1"
+                help="to estimate missing ones"/>
+
+            <param argument="Y" type="integer" value="" optional="True"
+                label="Specify how many replicates must contain data for a certain CpG position in group 2"
+                help="to estimate missing ones"/>
+
             <param name="opt_d" type="float" value="0.1"
                 label="The minimum mean methylation difference for calling DMRs"
                 help="-d, --minMethDiff"/>
diff -r 48462181c628 -r af2c31467ca0 tool_dependencies.xml
--- a/tool_dependencies.xml	Tue Feb 23 07:27:45 2016 -0500
+++ b/tool_dependencies.xml	Wed Jul 13 07:38:51 2016 -0400
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <tool_dependency>
     <package name="perl" version="5.18.1">
-        <repository changeset_revision="66db6ede3e0e" name="package_perl_5_18" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="95dad0955d7e" name="package_perl_5_18" owner="iuc" toolshed="https://testtoolshed.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" />