<?xml version="."?>
<tool id="bmsb" name="BMSB" version="1.0.0">
    <description></description>
    <requirements>
        <requirement type="package" version="1.3.0">r-optparse</requirement>
        <requirement type="package" version="1.20.0">r-getopt</requirement>
        <requirement type="package" version="0.9.19">r-jsonlite</requirement>
    </requirements>
    <command>
        <![CDATA[
            #import json
            Rscript $__tool_directory__/bmsb.R
            -o "$output"
            #if str($output_r_logging_cond.output_r_logging) == "yes":
                -s "true"
                -m "$output_r_log"
            #end if
            #if str($output_r_logging_cond.output_r_logging) == "yes":
                -e "true"
                -x "$output_ex_report"
            #end if
        ]]>
    </command>
    <inputs>
        <conditional name="output_r_logging_cond">
            <param name="output_r_logging" type="select" label="Output R logging?" help="Generate an additional dataset consisting of R messages.">
                <option value="yes" selected="True">Yes</option>
                <option value="no">No</option>
            </param>
            <when value="no"/>
            <when value="yes"/>
        </conditional>
    </inputs>
    <outputs>
        <data name="output_r_log" format="txt" label="${tool.name} on ${on_string}: R log">
            <filter>output_r_logging_cond['output_r_logging'] == "yes"</filter>
        </data>
        <data name="output_ex_report" format="json" label="${tool.name} on ${on_string}: Experiment report">
            <filter>output_experiment_report_cond['output_experiment_report'] == "yes"</filter>
        </data>
        <data name="output" format="RData"/>
    </outputs>
    <help>
**What it does**
 
BMSB prototype tool.
    </help>
    <citations>
        <citation></citation>
    </citations>
</tool>