<tool id="hicup_digester" name="Hicup Digester" version="@VERSION@+galaxy0">
    <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" />
    <command detect_errors="exit_code"><![CDATA[
        hicup_digester --re1 '$re1' --genome '$genome'
        #if $advanced_options.re2:
            --re2 '$advanced_options.re2'
        #end if
        #if str($input_files_digest.source) == "history":
            #for $file in $input_files_digest.own_file:
                '$file'
            #end for
        #else:
            '$reference_genome.index.fields.path'.fa
        #end if
    ]]></command>
    <inputs>
        <conditional name="input_files_digest">
            <param name="source" type="select" label="Will you select a reference genome from your history or use a genome which has a built-in index?" help="Built-ins were indexed using default options. See `Indexes` section of help below">
                <option value="indexed">Use a genome with a built-in index</option>
                <option value="history">Use a genome from the history</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" multiple="true" label="Select reference genome" />
                <!--<param name="own_file" type="data" format="fasta" metadata_name="dbkey" label="Select reference genome" />-->
            </when>
        </conditional>
        <param argument="--genome" type="text" label="Genome name"
            help="Name of the genome to be digested."/>
        <expand macro="re1" />
        <section name="advanced_options" title="Advanced options">
            <expand macro="re2" />
        </section>
    </inputs>
    <outputs>
        <data name="digest_file" format="tabular" from_work_dir="Digest_*" label="Digester File.txt"/>
    </outputs>
     <tests>
        <test>
            <param name="source" value="history"/>
            <param name="own_file" value="chr21And22FromHg38.fasta"/>
            <param name="re1" value="A^AGCTT"/>
            <param name="genome" value="chr21And22FromHg38"/>
            <output name="digest_file" file="digest_file.txt" lines_diff="0"/>
        </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 digister visit:https://www.bioinformatics.babraham.ac.uk/projects/hicup/read_the_docs/html/index.html#hicup-digester
    ]]></help>
    <expand macro="citation_hicup" />
</tool>