<macros>
   <xml name="requirements_hicup">
        <requirements>
            <requirement type="package" version="0.5.9">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>
        </requirements>
    </xml>
    <xml name="stdio">
        <stdio>
            <exit_code range="1:" />
        </stdio>
    </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_indices">
                    <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="filter_output">
        <data name="dataset_filt" format="sam" from_work_dir="dataset.filt.sam" label="filt.sam" />
        <data name="hicup_filter_summary" format="txt" from_work_dir="hicup_filter_summary.txt" label="hicup_filter_summary.txt" />
        <data name="contiguous_filter" format="sam" from_work_dir="hicup_filter_ditag_rejects/dataset.contiguous.filter.sam" label="contiguous.filter.sam" />
        <data name="re_ligation_filter" format="sam" from_work_dir="hicup_filter_ditag_rejects/dataset.re_ligation.filter.sam" label="re_ligation.filter.sam" />
        <data name="same_dangling_ends_filter" format="sam" from_work_dir="hicup_filter_ditag_rejects/dataset.same_dangling_ends.filter.sam" label="same_dangling_ends.filter.sam" />
        <data name="invalid_filter" format="sam" from_work_dir="hicup_filter_ditag_rejects/dataset.invalid.filter.sam" label="invalid.filter.sam" />
        <data name="same_circularised_filter" format="sam" from_work_dir="hicup_filter_ditag_rejects/dataset.same_circularised.filter.sam" label="same_circularised.filter.sam" />
        <data name="same_internal_filter" format="sam" from_work_dir="hicup_filter_ditag_rejects/dataset.same_internal.filter.sam" label="same_internal.filter.sam" />
        <data name="wrong_size_filter" format="sam" from_work_dir="hicup_filter_ditag_rejects/dataset.wrong_size.filter.sam" label="wrong_size.filter.sam"/>
        <data name="filter_piechart" format="svg" from_work_dir="filter_piechart.svg" label="Filter piechart.svg" />
    </xml>
    <xml name="mapper_output">
        <data name="hicup_mapper_summary" format="txt" from_work_dir="hicup_mapper_summary.txt" label="hicup_mapper_summary.txt"/>
        <data name="result_pair" format="sam" from_work_dir="result.pair.sam" label="pair.sam"/>
        <data name="dataset1_mapper_barchart" format="svg" from_work_dir="dataset1.mapper_barchart.svg" label="Mapper Dataset1 Barchart.svg" />
        <data name="dataset2_mapper_barchart" format="svg" from_work_dir="dataset2.mapper_barchart.svg" label="Mapper Dataset2 Barchart.svg" />
    </xml>
    <xml name="truncater_output">
        <data name="hicup_truncater_summary" format="txt" label="hicup_truncater_summary.txt" from_work_dir="hicup_truncater_summary.txt" />
        <data name="dataset1_trunc" format="fastq" label="Hicup Dataset1 Truncation" from_work_dir="dataset1.trunc.fastq" />
        <data name="dataset2_trunc" format="fastq" label="Hicup Dataset2 Truncation" from_work_dir="dataset2.trunc.fastq" />
        <data name="dataset1_truncater_barchart" format="svg" label="Hicup Dataset1 Truncation Barchart.svg" from_work_dir="dataset1.truncation_barchart.svg" />
        <data name="dataset2_truncater_barchart" format="svg" label="Hicup Dataset2 Truncation Barchart.svg" from_work_dir="dataset2.truncation_barchart.svg" />
        
    </xml>
    <xml name="input_files">
        <param name="input_first_sequence" type="data" format="fastq" label="First input sequence" help="The first sequence:"/>
        <param name="input_second_sequence" type="data" format="fastq" 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="digester_input">
        <param name="input_files_digest" type="data" multiple="true" format="fasta" label="Input DNA sequence files that should be digested"/>
        <param argument="--genome" type="text" label="Genome" help="Name of the genome to be digested (not the path to the genome 
        file or files, but the genome name to include in the output file)"/>
    </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>
    <xml name="deduplicator_output">
        <data name="cis_trans_piechart" format="svg" from_work_dir="deduplicator_cis_trans_piechart.svg" label="Hicup Deduplicator Cis Trans Piechart.svg"/>
        <data name="uniques_barchart" format="svg" from_work_dir="deduplicator_uniques_barchart.svg" label="Hicup Deduplicator Uniques Barchart.svg" />
        <data name="hicup_deduplicator_summary" format="txt" from_work_dir="hicup_deduplicator_summary.txt" label="Hicup Deduplicator Summary" />
    </xml>
</macros>