<tool id="cmeth" name="Cmeth" version="0.2.0">
    <description>BS-Seq analysis</description>
    <requirements>
        <requirement type="package" version="0.0.1">integration_jar</requirement>
    </requirements>
    <stdio>
        <!-- Wrapper ensures anything other than zero is an error -->
        <exit_code range="1:"/>
        <exit_code range=":-1"/>
    </stdio>
    <command interpreter="python">
        #if $action.selection == "analyze"
            cmeth_wrapper.py "${genome}" "${fdr}" analyze "${bam}"
        #else
            cmeth_wrapper.py "${genome}" "${fdr}" compare "${bam1}" "${bam2}"
        #end if
    </command>
    <inputs>
        <param name="genome" type="data" format="fasta" label="Genome build" description="Genome build reference"/>
        <param name="fdr" size="5" type="float" value="0.0001" label="FDR"/>
        <conditional name="action">
            <param name="selection" type="select" label="Action">
                <option value="analyze">Compute methylation</option>
                <option value="compare">Compare methylation</option>
            </param>
            <when value="analyze">
                <param name="bam" type="data" format="bam" label="Aligned BS-Seq bam" description="BAM BS-Seq Aligned reads to process"/>
            </when>
            <when value="compare">
                <param name="bam1" type="data" format="bam" label="Aligned BS-Seq bam1" description="BAM BS-Seq Aligned reads to process 1"/>
                <param name="bam2" type="data" format="bam" label="Aligned BS-Seq bam2" description="BAM BS-Seq Aligned reads to process 2"/>
            </when>
        </conditional>
    </inputs>
    <outputs>
        #if $action.selection == "analyze"
        <data name="result" format="csv" label="CG_unmethylated.csv"/>
        #else
        <data name="result" format="csv" label="CG_emr.csv"/>
        #end if
    </outputs>
    <help>
Cmeth is a tool for analyzing and comparing cytosine methylation from WGBS (whole-genome bisulfite sequencing) data.
Both procedures rely on the nonparametric Bayesian switching HMM.
https://github.com/JetBrains-Research/cmeth
    </help>
</tool>