<?xml version="1.0"?>
<macros>
    <token name="@TOOL_VERSION@">0.4.3</token>
    <token name="@VERSION_SUFFIX@">1</token>
    <token name="@PROFILE@">20.05</token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@TOOL_VERSION@">slamdunk</requirement>
        </requirements>
    </xml>
    <xml name="reference_files">
        <conditional name="reference_source">
            <param name="reference_source_selector" type="select" label="Reference genome FASTA file" help="Select a built-in FASTA file (if available) or one from the history">
                <option value="cached">Use a built-in FASTA</option>
                <option value="history">Use a FASTA from history</option>
            </param>
            <when value="cached">
                <param name="ref_file" argument="--reference" type="select" label="Use built-in FASTA" help="Select genome from the list">
                    <options from_data_table="all_fasta">
                        <filter type="sort_by" column="2" />
                        <validator type="no_options" message="No reference genomes are available" />
                    </options>
                    <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
                </param>
            </when>
            <when value="history">
                <param name="ref_file" argument="--reference" type="data" format="fasta" label="Use the following dataset as the FASTA" help="You can upload a FASTA sequence to the history and use it as reference" />
            </when>
        </conditional>
        <param argument="--reference" type="data" format="bed" label="Reference 3'UTRs BED file" />
    </xml>
    <xml name="citations">
        <citation type="doi">
            10.1186/s12859-019-2849-7
        </citation>
    </xml>
</macros>