# HG changeset patch
# User rnateam
# Date 1551643044 18000
# Node ID efc829e9f2929c1858785acab4e3273af59c182d
# Parent  af2c31467ca05c7b863e30e144bb4db583e7c16d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/metilene commit a712270ae9e703969bde0dc3268b047b6aab396f

diff -r af2c31467ca0 -r efc829e9f292 metilene.xml
--- a/metilene.xml	Wed Jul 13 07:38:51 2016 -0400
+++ b/metilene.xml	Sun Mar 03 14:57:24 2019 -0500
@@ -1,17 +1,13 @@
 <?xml version="1.0" encoding="utf-8"?>
-<tool id="metilene" name="metilene" version="0.2.6.0">
+<tool id="metilene" name="metilene" version="0.2.6.1">
     <description>
         calling differentially methylated regions from bisulfite sequencing data
     </description>
     <requirements>
         <requirement type="package" version="0.2.6">metilene</requirement>
-        <requirement type="package" version="5.18.1">perl</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="3.5.1">r-base</requirement>
         <requirement type="package" version="2.24">bedtools</requirement>
-        <requirement type="package" version="8.22">gnu_coreutils</requirement>
+        <requirement type="package" version="8.25">coreutils</requirement>
     </requirements>
     <stdio>
         <exit_code range=":-1"/>
@@ -22,8 +18,8 @@
     ## preprocessing
     ## generate metilene_g1_g2.input from multiple bedgraph files
     metilene_input.pl
-        --in1 "$opt_in1"
-        --in2 "$opt_in2"
+        --in1 '$opt_in1'
+        --in2 '$opt_in2'
         >/dev/null 
        ##2>/dev/null
     &&
@@ -48,7 +44,7 @@
 
         -v $Options.opt_v
         metilene_g1_g2.input
-        > $output_bedlike
+        > '$output_bedlike'
         ##2> /dev/null
     &&
     ## postprocessing
@@ -56,7 +52,7 @@
     &&
     ## write to job directory
     metilene_output.pl
-        -q $output_bedlike
+        -q '$output_bedlike'
         -p 0.05
         -o ./metilene 
         ##>/dev/null 
diff -r af2c31467ca0 -r efc829e9f292 tool_dependencies.xml
--- a/tool_dependencies.xml	Wed Jul 13 07:38:51 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,47 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <package name="perl" version="5.18.1">
-        <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" />
-    </package>
-    <package name="gnu_coreutils" version="8.22">
-        <repository changeset_revision="8b60cf3e0c07" name="package_gnu_coreutils_8_22" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="ggplot2" version="0.9.3">
-        <repository changeset_revision="ade406d47752" name="package_r_ggplot2_0_9_3" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="metilene" version="0.2-4">
-        <install version="1.0">
-            <actions>
-                <action sha256sum="7430b4c2af4f43d389ad690dfe42c9ce7a63b2bff4ff0ac59afc0f1ec7e600f2" type="download_by_url">
-                    https://depot.galaxyproject.org/software/metilene/metilene_0.2-4_src_all.tar.gz
-                </action>
-                <action type="shell_command">make</action>
-                <!-- move binary and scripts to installation bin directory -->
-                <action type="move_file">
-                    <source>metilene</source>
-                    <destination>$INSTALL_DIR/bin</destination>
-                </action>
-                <action type="move_file">
-                    <source>metilene_input.pl</source>
-                    <destination>$INSTALL_DIR/bin</destination>
-                </action>
-                <action type="move_file">
-                    <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>
-
-                <action type="set_environment">
-                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
-                </action>
-            </actions>
-        </install>
-        <readme>Metilene is precompiled for Linux</readme>
-    </package>
-</tool_dependency>