<tool id="hicup_truncater" name="Hicup Truncater" version="@VERSION@+galaxy0">
    <description>terminates sequence reads at specified Hi-C ligation junctions.</description>
    <macros>
        <import>hicup_macros.xml</import>
    </macros>
    <expand macro="requirements_hicup"/>
    <command detect_errors="exit_code"><![CDATA[
        ##Dealing with inputs
        @PAIRED-END_INPUT@
        
        hicup_truncater --re1 '$re1' --zip $advanced_options.nofill
            '$read1'
            '$read2'
    ]]></command>
    <inputs>
        <expand macro="input_paired"/>
        <expand macro="re1"/>
        <section name="advanced_options" title="Advanced options">
            <expand macro="no_fill"/>
        </section>
    </inputs>
    <outputs>
        <data name="dataset1_trunc" format="fastq.gz" label="Hicup Truncation on ${on_string}: Read 1 Output" from_work_dir="dataset1*.trunc.fastq.gz">
            <filter>library['type'] != 'paired_collection'</filter>
        </data>
        <data name="dataset2_trunc" format="fastq.gz" label="Hicup Truncation on ${on_string}: Read 2 Output" from_work_dir="dataset2*.trunc.fastq.gz">
            <filter>library['type'] != 'paired_collection'</filter>
        </data>
        <collection name="dataset_trunc_pairs" type="paired" format="fastq.gz" label="Hicup Truncation on ${on_string}">
            <filter>library['type'] == 'paired_collection' and 'multiple_output' not in output_selector</filter>
            <data name="forward" from_work_dir="dataset1*.trunc.fastq.gz"/>
            <data name="reverse" from_work_dir="dataset2*.trunc.fastq.gz"/>
        </collection>
        <data name="hicup_truncater_summary" format="tabular" label="hicup_truncater_summary.txt" from_work_dir="hicup_truncater_summary*.txt"/>
        <collection type="list" name="truncation_barchart" label="Truncation Barchart.svg">
            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.truncation_barchart\.svg$" directory="./" ext="svg"/>
        </collection>
    </outputs>
    <tests>
        <test>
            <conditional name="library">
                <param name="type" value="paired"/>
                <param name="input_1" value="dataset1.fastq" ftype="fastq"/>
                <param name="input_2" value="dataset2.fastq" ftype="fastq"/>
            </conditional>
            <param name="re1" value="A^AGCTT"/>
            <output name="hicup_truncater_summary">
                <assert_contents>
                    <has_text_matching expression="\s+99742\s+7230\s+7.25\s+92512\s+92.75\s+22.45"/>
                    <has_text_matching expression="\s+99742\s+7114\s+7.13\s+92628\s+92.87\s+22.63"/>
                </assert_contents>
            </output>
            <output name="dataset1_trunc" file="dataset1.trunc.fastq.gz" decompress="true"/>
            <output name="dataset2_trunc" file="dataset2.trunc.fastq.gz" decompress="true"/>
            <output_collection name="truncation_barchart" count="2">
                <element name="dataset1.fq" file="dataset1.truncation_barchart.svg" ftype="svg" compare="sim_size"/>
                <element name="dataset2.fq" file="dataset2.truncation_barchart.svg" ftype="svg" compare="sim_size"/>
            </output_collection>
        </test>
        <test>
            <conditional name="library">
                <param name="type" value="paired_collection"/>
                <param name="input_1">
                    <collection type="paired">
                        <element name="forward" ftype="fastq" value="dataset1.fastq"/>
                        <element name="reverse" ftype="fastq" value="dataset2.fastq"/>
                    </collection>
                </param>
            </conditional>
            <param name="re1" value="A^AGCTT"/>
            <output name="hicup_truncater_summary">
                <assert_contents>
                    <has_text_matching expression="\s+99742\s+7230\s+7.25\s+92512\s+92.75\s+22.45"/>
                    <has_text_matching expression="\s+99742\s+7114\s+7.13\s+92628\s+92.87\s+22.63"/>
                </assert_contents>
            </output>
            <output_collection name="dataset_trunc_pairs" type="paired" count="2">
                <element name="forward" decompress="true" file="dataset1.trunc.fastq.gz" ftype="fastq.gz"/>
                <element name="reverse" decompress="true" file="dataset2.trunc.fastq.gz" ftype="fastq.gz"/>
            </output_collection>
            <output_collection name="truncation_barchart" count="2">
                <element name="dataset1.fq" file="dataset1.truncation_barchart.svg" ftype="svg" compare="sim_size"/>
                <element name="dataset2.fq" file="dataset2.truncation_barchart.svg" ftype="svg" compare="sim_size"/>
            </output_collection>
        </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 truncater visit: https://www.bioinformatics.babraham.ac.uk/projects/hicup/read_the_docs/html/index.html#hicup-truncater
    ]]></help>
    <expand macro="citation_hicup"/>
</tool>