<?xml version="1.0" encoding="utf-8"?>
<tool id="metilene" name="metilene" version="0.2-4.1">
    <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="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
        #if $B:
            -f 2
            -B "$B"
        #else:
            -f 1
        #end if
        -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/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/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"
                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>