<tool id="create_genome_tracks" name="Create genome tracks" version="1.0.0">
    <description>from IDEAS statistics</description>
    <requirements>
        <requirement type="package" version="2.4.27">bedops</requirement>
        <requirement type="package" version="1.10.4">r-data.table</requirement>
         <requirement type="package" version="1.4.4">r-optparse</requirement>
         <requirement type="package" version="332">ucsc-bedtobigbed</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
Rscript '$__tool_directory__/create_genome_tracks.R'
-b $parameter_file.metadata.dbkey
-c '$chromInfo'
-f test
-p '$parameter_file'
-s '$state_file'
-t 'http://bx.psu.edu/~yuzhang/tmp/'
-u '$output_track_db'
-v '$output_build'
-w '$output_hub']]></command>
    <inputs>
        <param name="state_file" type="data" format="txt" label="IDEAS epigenetic states and position classes dataset">
            <validator type="empty_field"/>
            <validator type="unspecified_build"/>
        </param>
        <param name="parameter_file" type="data" format="tabular" label="IDEAS epigenetic state frequency, mean and variance parameters dataset">
            <validator type="empty_field"/>
            <validator type="unspecified_build"/>
        </param>
    </inputs>
    <outputs>
        <data name="output_track_db" format="bigbed" label="${tool.name} (track db) on ${on_string}"/>
        <data name="output_build" format="txt" label="${tool.name} (genome build) on ${on_string}"/>
        <data name="output_hub" format="txt" label="${tool.name} (hub) on ${on_string}"/>
    </outputs>
    <tests>
        <test>
        </test>
    </tests>
    <help>
**What it does**

-----

**Required options**
 
    </help>
    <citations>
        <citation type="doi">10.1093/nar/gkw278</citation>
    </citations>
</tool>