<macros>
    <token name="@VERSION@">0.6.1</token>
    <xml name="requirements_hicup">
        <requirements>
            <requirement type="package" version="@VERSION@">hicup</requirement>
            <requirement type="package" version="2.2.6">bowtie2</requirement>
            <requirement type="package" version="1.2">samtools</requirement>
            <requirement type="package" version="0.13.1">docutils</requirement>
            <yield/>
        </requirements>
        <version_command>hicup --version</version_command>
    </xml>
    <xml name="citation_hicup">
        <citations>
            <citation type="doi">10.12688/f1000research.7334.1</citation>
        </citations>
    </xml>
    <xml name="reference_genome_macro">
        <conditional name="reference_genome">
            <param name="source" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options. See `Indexes` section of help below">
                <option value="indexed">Use a built-in genome index</option>
                <option value="history">Use a genome from the history and build index</option>
            </param>
            <when value="indexed">
                <param name="index" type="select" label="Select reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
                <options from_data_table="bowtie2_indexes">
                    <filter type="sort_by" column="2"/>
                    <validator type="no_options" message="No indexes are available for the selected input dataset"/>
                </options>
                </param>
            </when>
            <when value="history">
                <param name="own_file" type="data" format="fasta" label="Select reference genome" />
                <!--<param name="own_file" type="data" format="fasta" metadata_name="dbkey" label="Select reference genome" />-->
            </when>
        </conditional>
    </xml>
    <xml name="input_files">
        <param name="input_first_sequence" type="data" format="fastq,fastq.gz" label="First input sequence" help="The first sequence:"/>
        <param name="input_second_sequence" type="data" format="fastq,fastq.gz" label="Second input sequence" help="The second sequence:"/>
    </xml>
    <xml name="re1">
        <param argument="--re1" type="text" value="" label="Restriction enzyme recognition sequence" help="Restriction enzyme recognition sequence"/>
    </xml>
    <xml name="re2">
        <param argument="--re2" type="text" value="" label="Restriction enzyme instead of sonication to shorten di-tags."
            help="To specify a restriction enzyme instead of sonication to shorten di-tags. This restriction site does NOT form a Hi-C ligation junction. 2 .g. AG^CT,AluI. Typically the sonication protocol is followed."/>
    </xml>
    <xml name="filter_longest_shortest">
        <param argument="--longest" type="text" value="" label="Max insert size" help="Maximum allowable insert size (bps)"/>
        <param argument="--shortest" type="text" value="" label="Min insert size" help="Minimum allowable insert size (bps)"/>
    </xml>
    <xml name="no_fill">
        <param argument="--nofill" type="boolean" value="false" truevalue="--nofill" falsevalue="" label="No fill"
            help="Hi-C protocol did NOT include a fill-in of sticky ends prior to re-ligation and therefore reads shall be truncated at the restriction site sequence"/>
    </xml>
</macros>