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<tool id="most" name="MOST">
	<description>Determine MLST from sequencing reads</description>

    <requirements>
        <requirement type="package" version="2.7.10">python</requirement>
        <requirement type="package" version="3.2.3">lxml</requirement>
        <requirement type="package" version="3.11">pyyaml</requirement>
        <requirement type="package" version="1.9">numpy</requirement>
        <requirement type="package" version="1.66">biopython</requirement>
        <requirement type="package" version="2.1.0">bowtie2</requirement>
        <requirement type="package" version="0.1.18">samtools</requirement>
        <requirement type="package" version="5.0.0">emboss</requirement>
        <requirement type="package" version="2.2.27">blast+</requirement>
        <requirement type="package" version="1.0">phemost</requirement>
    </requirements>

	<command interpreter="bash">
	MOST.sh
	$fwd_file
	$rev_file
	$out1
	$out2
	"${organism.fields.file_path}"
	</command>

	<inputs>
        <param name="fwd_file" type="data" format="fastq" label="Read dataset for direction 1" help="Select fastq R1 here."/>
        <param name="rev_file" type="data" format="fastq" label="Read dataset for direction 2" help="Select fastq R2 here."/>
        <param name="organism" type="select" label="Select an organism">
            <options from_data_table="mlst_data">
                <column name="value" index="0"/>
                <column name="dbkey" index="1"/>
                <column name="name" index="2"/>
                <column name="time_stamp" index="3"/>
                <column name="file_path" index="4"/>
                <validator type="no_options" message="No indexes are available" />
            </options>
        </param>
	</inputs>

	<outputs>
	    <data name="out1" format="xml" label="${fwd_file.name}: MLST result XML"/>
	    <data name="out2" format="csv" label="${fwd_file.name}: MLST result CSV"/>
	</outputs>

	<help>
		https://github.com/phe-bioinformatics/MOST
	</help>
</tool>