<tool id="busco" name="Busco" version="2.0">
    <description>assess genome assembly and annotation completeness</description>

    <requirements>
        <requirement type="package" version="2.0">busco</requirement>
    </requirements>

    <command><![CDATA[
        BUSCO.py
        --in '${input}'
        --lineage '${lineage.fields.path}'
        --mode '${mode}'
        -o "busco_galaxy"
        --cpu \${GALAXY_SLOTS:-4}
        --evalue ${adv.evalue}
        ${adv.long}
        --limit ${adv.limit}
        #if $adv.species:
            --species '${adv.species}'
        #end if
        --tarzip
    ]]></command>

    <inputs>

        <param type="data" name="input" format="fasta" label="Sequences to analyse" help="genome, transcriptome or proteome" />

        <param argument="--mode" type="select" label="Mode">
            <option value="geno">Genome</option>
            <option value="tran">Transcriptome</option>
            <option value="prot">Proteome</option>
        </param>

        <param argument="--lineage" type="select" label="Lineage">
            <options from_data_table="busco">
                <filter type="sort_by" column="2" />
                <validator type="no_options" message="No indexes are available" />
            </options>
        </param>

        <section name="adv" title="Advanced Options" expanded="False">
            <param argument="--evalue" type="float" value="0.01" label="E-value cutoff for BLAST searches."/>
            <param argument="--limit" type="integer" value="3" label="How many candidate regions to consider"/>
            <param argument="--species" type="text" optional="True" label="Name of existing Augustus species gene finding metaparameters"/>
            <param argument="--long" type="boolean" checked="false" truevalue="--long" falsevalue="" label="Optimization mode Augustus self-training" help="Adds considerably to run time, but can improve results for some non-model organisms"/>
        </section>
    </inputs>
    <outputs>
        <data name='busco_sum' format='txt' label="${tool.name} on ${on_string}: short summary" from_work_dir="run_busco_galaxy/short_summary_busco_galaxy.txt"/>
        <data name='busco_table' format='tabular' label="${tool.name} on ${on_string}: full table" from_work_dir="run_busco_galaxy/full_table_busco_galaxy.tsv"/>
        <data name='busco_missing' format='tabular' label="${tool.name} on ${on_string}: missing buscos" from_work_dir="run_busco_galaxy/missing_busco_list_busco_galaxy.tsv"/>
    </outputs>
    <tests>
        <test>
            <param name="input" value="genome.fa"/>
            <param name="lineage" value="arthropoda_2.0"/>
            <param name="mode" value="geno"/>
            <output name="busco_sum" file="genome_results/short_summary" compare="diff" lines_diff="4"/>
            <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="4"/>
            <output name="busco_missing" file="genome_results/missing_buscos_list" compare="diff" lines_diff="4"/>
        </test>
        <test>
            <param name="input" value="proteome.fa"/>
            <param name="lineage" value="arthropoda_2.0"/>
            <param name="mode" value="prot"/>
            <output name="busco_sum" file="proteome_results/short_summary" compare="diff" lines_diff="4"/>
            <output name="busco_table" file="proteome_results/full_table" compare="diff" lines_diff="4"/>
            <output name="busco_missing" file="proteome_results/missing_buscos_list" compare="diff" lines_diff="4"/>
        </test>
        <test>
            <param name="input" value="transcriptome.fa"/>
            <param name="lineage" value="arthropoda_2.0"/>
            <param name="mode" value="tran"/>
            <output name="busco_sum" file="transcriptome_results/short_summary" compare="diff" lines_diff="4"/>
            <output name="busco_table" file="transcriptome_results/full_table" compare="diff" lines_diff="4"/>
            <output name="busco_missing" file="transcriptome_results/missing_buscos_list" compare="diff" lines_diff="4"/>
        </test>
    </tests>
    <help>
        BUSCO: assessing genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs

        .. _BUSCO: http://busco.ezlab.org/
    </help>

     <citations>
        <citation type="doi">doi:10.1093/bioinformatics/btv351</citation>
    </citations>
</tool>