<?xml version="1.0"?>
<macros>
    <token name="@VERSION@">0.43.1</token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@VERSION@">kallisto</requirement>
            <requirement type="package" version="1.5">samtools</requirement>
        </requirements>
    </xml>
    <xml name="citations">
        <citations>
            <citation type="doi">doi:10.1038/nbt.3519</citation>
        </citations>
    </xml>
    <xml name="reference_input">
        <conditional name="reference_transcriptome">
            <param name="reference_transcriptome_source" type="select" label="Reference transcriptome for quantification">
                <option value="indexed" selected="true">Use a built-in transcriptome</option>
                <option value="history">Use a transcriptome from history</option>
            </param>
            <when value="indexed">
                <param name="index" type="select" label="Select a reference transcriptome" help="If your transcriptome of interest is not listed, contact your Galaxy administrator">
                    <options from_data_table="kallisto_indexes">
                        <filter type="sort_by" column="2" />
                        <validator type="no_options" message="No transcriptomes are available for the selected input dataset" />
                    </options>
                </param>
            </when>
            <when value="history">
                <param name="reference" type="data" format="fasta" label="FASTA reference transcriptome" />
            </when>
        </conditional>
    </xml>
</macros>