--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/metilene.xml	Thu Dec 17 17:10:08 2015 -0500
@@ -0,0 +1,127 @@
+<?xml version="1.0" encoding="utf-8"?>
+<tool id="metilene" name="metilene" version="0.2-4.0">
+    <description>
+        calling differentially methylated regions from bisulfite sequencing data
+    </description>
+    <requirements>
+        <requirement type="package" version="0.2-4">metilene</requirement>
+        <requirement type="package" version="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="2.24">bedtools</requirement>
+        <requirement type="package" version="8.22">gnu_coreutils</requirement>
+    </requirements>
+    <stdio>
+        <exit_code range=":-1"/>
+        <exit_code range="1:" />
+    </stdio>
+    <version_command>echo "0.2-4"</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
+    &&
+    ## metilene main program
+    metilene
+        -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>/dev/null
+    &&
+    ## postprocessing
+    cut -f1-4 $output_bedlike > $output_bedgraph 2>/dev/null
+    &&
+    ## write to job directory
+    metilene_output.pl
+        -q $output_bedlike
+        -p 0.05
+        -o ./metilene >/dev/null 2>/dev/null
+    ]]></command>
+    <inputs>
+        <!-- input bedgraph files 1 -->
+        <param name="opt_in1" type="data" format="bed,bedgraph" multiple="true"
+            label="Input group 1"
+            help="set of sorted bedgraph input profiles of group 1" />
+        <!-- input bedgraph files 2 -->
+        <param name="opt_in2" type="data" format="bed,bedgraph" multiple="true"
+            label="Input group 2"
+            help="set of sorted bedgraph input profiles of group 2" />
+        
+        <!-- Advanced parameters (folded) -->
+        <section name="Options" title="Advanced Options" expanded="False">
+            <param name="opt_M" type="integer" value="300"
+                label="The allowed nt distance between two CpGs within a DMR"
+                help="-M, --maxdist"/>
+
+            <param name="opt_m" type="integer" value="10"
+                label="The minimum # of CpGs in a DMR"
+                help="-m, --mincpgs"/>
+
+            <param name="opt_d" type="float" value="0.1"
+                label="The minimum mean methylation difference for calling DMRs"
+                help="-d, --minMethDiff"/>
+
+            <param name="opt_v" type="float" value="0.7" label="Stringency of the valley filter (0.0 - 1.0)"
+                help="-v, --valley">
+                <validator type="in_range" min="0.0" max="1.0" message="Valley filter value must be in [0,1]." />
+            </param>
+        </section>
+    </inputs>
+    <outputs>
+        <!-- finally: for bed-like use format=tabular -->
+        <data format="tabular" name="output_bedlike" 
+              label="${tool.name} on ${on_string}" />
+        <data format="bedgraph" name="output_bedgraph" 
+              label="${tool.name} bedgraph on ${on_string}" />
+        <data format="bedgraph" name="output_qval_bedgraph" 
+              label="${tool.name} qval&lt;0.05 bedgraph on ${on_string}"
+              from_work_dir="metilene_qval.0.05.bedgraph" />
+        <data format="pdf" name="output_qval_pdf" 
+              label="${tool.name} qval&lt;0.05 plots on ${on_string}"
+              from_work_dir="metilene_qval.0.05.pdf" />
+        <data format="bedgraph" name="output_qval_out" 
+              label="${tool.name} qval&lt;0.05 out on ${on_string}"
+              from_work_dir="metilene_qval.0.05.out" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="opt_in1" value="example_S1.bedgraph,example_S2.bedgraph,example_S3.bedgraph,example_S4.bedgraph" />
+            <param name="opt_in2" value="example_S5.bedgraph,example_S6.bedgraph,example_S7.bedgraph,example_S8.bedgraph" />
+            <output name="output_bedlike" file="metilene.out" />
+        </test>
+    </tests>
+    <help><![CDATA[
+**Fast and sensitive calling of differentially methylated regions
+from bisulfite sequencing data**
+
+Detailed documentation of the stand-alone tool metilene is available at
+.. __: http://www.bioinf.uni-leipzig.de/Software/metilene/manual.pdf
+
+The software metilene is available for download at
+.. __: http://www.bioinf.uni-leipzig.de/Software/metilene/
+    ]]></help>
+
+    <citations>
+        <citation type="bibtex">@Article{Juhling_Kretzmer_Bernhart-metil_Fast_and-2015,
+  author =   {Juhling, Frank and Kretzmer, Helene and Bernhart, Stephan 
+                  H. and Otto, Christian and Stadler, Peter F. and Hoffmann, 
+                  Steve},
+  title =    {metilene: {Fast} and sensitive calling of differentially 
+                  methylated regions from bisulfite sequencing data},
+  page =         {[Epub ahead of print]},
+  journal =  {Genome Res},
+  year =     {2015},
+  pmid =     {26631489},
+  doi =      {10.1101/gr.196394.115},
+  issn =     {1088-9051},
+  issn =     {1549-5469}}</citation>
+    </citations>
+</tool>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/example_S1.bedgraph	Thu Dec 17 17:10:08 2015 -0500
@@ -0,0 +1,10699 @@
+#chrom	start	end	S1
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