<tool id="hicup_digester" name="Hicup Digester" version="0.1.0">
    <description>cuts throughout a selected genome at one or two specified restriction sites.</description>
    <macros>
        <import>hicup_macros.xml</import>
    </macros>
    <expand macro="requirements_hicup" />
    <expand macro="stdio" />

    <command><![CDATA[
        hicup_digester --re1 '$re1' --genome '$genome'
        #if $advanced_options.re2:
            --re2 '$advanced_options.re2'
        #end if
        #for $file in $input_files_digest:
            $file
        #end for
        && mv *Digest_* digester_file.txt
    ]]></command>
    <inputs>
        <expand macro="digester_input" />
        <expand macro="re1" />   
        <section name="advanced_options" title="Advanced options">
            <expand macro="re2" />
        </section>
    </inputs>
    <outputs>
        <data name="digest_file" format="txt" from_work_dir="digester_file.txt" label="Digester File.txt"/>
    </outputs>
     <tests>
        <test>
            <param name="input_files_digest" value="chr1.fa"/>
            <param name="re1" value="A^AGCTT"/>
            <param name="genome" value="human"/>
            <output name="digest_file" file="digester_file.txt" lines_diff="4"/>
        </test>
    </tests>
    <help><![CDATA[

    For help please consult the documentation of HiCUP: http://www.bioinformatics.babraham.ac.uk/projects/hicup/overview/

    To get more information about the digister visit: http://www.bioinformatics.babraham.ac.uk/projects/hicup/scripts_description/#Digester
    ]]></help>
    <expand macro="citation_hicup" />
</tool>