<tool id="hicup_deduplicator" name="Hicup Deduplicator" version="@VERSION@+galaxy0" profile="18.01">
    <description>removes duplicated di-tags (retaining one copy of each) from the data set.</description>
    <macros>
        <import>hicup_macros.xml</import>
    </macros>
    <expand macro="requirements_hicup" />
    <command detect_errors="exit_code"><![CDATA[
        #if $input_file.ext != 'sam':
            ln -s '$input_file' input.bam  &&
        #end if
        hicup_deduplicator --zip --quiet
        #if $input_file.ext != 'sam':
            input.bam
        #else
            '$input_file'
        #end if
    ]]></command>
    <inputs>
        <param name="input_file" type="data" format="qname_sorted.bam,sam" label="Input file(s)" help="Input files in BAM or SAM format."/>
    </inputs>
    <outputs>
        <data name="dedup_result" format="qname_sorted.bam" label="Deduplicator Result" from_work_dir="*dedup*.bam" />
        <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="tabular" from_work_dir="hicup_deduplicator_summary*.txt" label="Hicup Deduplicator Summary" />
    </outputs>
    <tests>
        <test>
            <param name="input_file" value="dataset1_2.filt.bam" ftype="qname_sorted.bam"/>
            <output name="dedup_result" file="dataset1_2.hicup.bam" compare="sim_size" ftype="qname_sorted.bam"/>
            <output name="cis_trans_piechart" file="dataset1_2.filt.bam.deduplicator_cis_trans_piechart.svg" ftype="svg" compare="sim_size"/>
            <output name="uniques_barchart" file="dataset1_2.filt.bam.deduplicator_uniques_barchart.svg" ftype="svg" compare="sim_size"/>
            <output name="hicup_deduplicator_summary">
                <assert_contents>
                    <has_text_matching expression="\s+544\s+544\s+44\s+440\s+60"/>
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="input_file" value="dataset1_2.filt.sam" ftype="sam"/>
            <output name="dedup_result" file="dataset1_2.hicup.bam" compare="sim_size" ftype="qname_sorted.bam"/>
            <output name="cis_trans_piechart" file="dataset1_2.filt.bam.deduplicator_cis_trans_piechart.svg" ftype="svg" compare="sim_size" delta="50000" />
            <output name="uniques_barchart" file="dataset1_2.filt.bam.deduplicator_uniques_barchart.svg" ftype="svg" compare="sim_size"/>
            <output name="hicup_deduplicator_summary">
                <assert_contents>
                    <has_text_matching expression="\s+544\s+544\s+44\s+440\s+60"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[

    For help please consult the documentation of HiCUP: https://www.bioinformatics.babraham.ac.uk/projects/hicup/read_the_docs/html/index.html

    To get more information about the deduplicator visit: https://www.bioinformatics.babraham.ac.uk/projects/hicup/read_the_docs/html/index.html#hicup-deduplicator
    ]]></help>
    <expand macro="citation_hicup" />
</tool>