# HG changeset patch
# User rnateam
# Date 1455833782 18000
# Node ID a538bbdae31b16b2c8afe56c9fc0cf7c460a7082
# Parent  0d988a56e3320809d3880465320204dba11f7a51
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/metilene commit f332463404ef478e78d3ff4583b806dd68dfd3af-dirty

diff -r 0d988a56e332 -r a538bbdae31b metilene.xml
--- a/metilene.xml	Thu Dec 17 17:10:08 2015 -0500
+++ b/metilene.xml	Thu Feb 18 17:16:22 2016 -0500
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="utf-8"?>
-<tool id="metilene" name="metilene" version="0.2-4.0">
+<tool id="metilene" name="metilene" version="0.2-4.1">
     <description>
         calling differentially methylated regions from bisulfite sequencing data
     </description>
@@ -20,8 +20,8 @@
     ## 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
     &&
     ## metilene main program
@@ -30,11 +30,16 @@
         -m $Options.opt_m
         -d $Options.opt_d
         -t 1
-        -f 1
+        #if $B:
+            -f 2
+            -B "$B"
+        #else:
+            -f 1
+        #end if
         -v $Options.opt_v
         metilene_g1_g2.input
-        >$output_bedlike
-        2>/dev/null
+        > $output_bedlike
+        2> /dev/null
     &&
     ## postprocessing
     cut -f1-4 $output_bedlike > $output_bedgraph 2>/dev/null
@@ -49,12 +54,16 @@
         <!-- input bedgraph files 1 -->
         <param name="opt_in1" type="data" format="bed,bedgraph" multiple="true"
             label="Input group 1"
-            help="set of sorted bedgraph input profiles of group 1" />
+            help="Set of sorted bedgraph/bed input profiles of group 1" />
         <!-- input bedgraph files 2 -->
         <param name="opt_in2" type="data" format="bed,bedgraph" multiple="true"
             label="Input group 2"
-            help="set of sorted bedgraph input profiles of group 2" />
-        
+            help="Set of sorted bedgraph/bed input profiles of group 2" />
+
+        <param argument="-B" type="data" format="bed" optional="True"
+            label="BED file containing regions of interest"
+            help="Regions that should be checked for differential methylation." />
+
         <!-- Advanced parameters (folded) -->
         <section name="Options" title="Advanced Options" expanded="False">
             <param name="opt_M" type="integer" value="300"
diff -r 0d988a56e332 -r a538bbdae31b tool_dependencies.xml
--- a/tool_dependencies.xml	Thu Dec 17 17:10:08 2015 -0500
+++ b/tool_dependencies.xml	Thu Feb 18 17:16:22 2016 -0500
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <tool_dependency>
     <package name="perl" version="5.18.1">
-        <repository changeset_revision="8b3509930a44" name="package_perl_5_18" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="d905bb415eca" name="package_perl_5_18" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
     <package name="R" version="3.2.1">
         <repository changeset_revision="d0bf97420fb5" name="package_r_3_2_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />