<tool id="busco" name="Busco" version="3.0.2">
    <description>assess genome assembly and annotation completeness</description>
    <requirements>
        <requirement type="package" version="3.0.2">busco</requirement>
        <requirement type="package" version="2.2.1">r-ggplot2</requirement>
    </requirements>
    <command><![CDATA[
        export BUSCO_CONFIG_FILE='busco_config.ini'

        &&

        if [ -z "\$AUGUSTUS_CONFIG_PATH" ] ; then BUSCO_PATH=\$(dirname \$(which run_BUSCO.py)) ; export AUGUSTUS_CONFIG_PATH=\$(realpath \${BUSCO_PATH}/../config) ; fi &&
        cp -r "\$AUGUSTUS_CONFIG_PATH/" augustus_dir/ &&
        export AUGUSTUS_CONFIG_PATH=`pwd`/augustus_dir/ &&

        #if $adv.aug_prediction.augustus_mode == 'history':
            ## Using an augustus model from history, we need to unzip it and let augustus find it

            mkdir -p 'augustus_dir/species/' &&

            tar -C 'augustus_dir/species/' -xzvf '${adv.aug_prediction.augustus_model}' > /dev/null &&
        #end if

        run_BUSCO.py
        --in '${input}'
        --lineage_path '${lineage_path.fields.path}/${lineage_path.fields.value}'
        --mode '${mode}'
        -o "busco_galaxy"
        --cpu \${GALAXY_SLOTS:-4}
        --evalue ${adv.evalue}
        ${adv.long}
        --limit ${adv.limit}
        #if $adv.aug_prediction.augustus_mode == 'builtin':
            --species '${adv.aug_prediction.augustus_species}'
        #else if $adv.aug_prediction.augustus_mode == 'history':
            --species local
        #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_path" 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"/>

            <conditional name="aug_prediction">
                <param name="augustus_mode" type="select" label="Augustus species model">
                    <option value="no" selected="true">Use the default species for selected lineage</option>
                    <option value="builtin">Use another predefined species model</option>
                    <option value="history">Use a custom species model</option>
                </param>
                <when value="no"/>
                <when value="history">
                    <param name="augustus_model" type="data" format="augustus" label="Augustus model"/>
                </when>
                <when value="builtin">
                    <param name="augustus_species" type="select" label="Augustus species model">
                        <!-- If you update this list, please also update it in maker and augustus tools (../maker/maker.xml and ../augustus/augustus.xml) -->
                        <option value="human">Homo sapiens</option>
                        <option value="fly">Drosophila melanogaster</option>
                        <option value="arabidopsis">Arabidopsis thaliana</option>
                        <option value="brugia ">Brugia malayi</option>
                        <option value="aedes">Aedes aegypti</option>
                        <option value="tribolium2012">Tribolium castaneum</option>
                        <option value="schistosoma">Schistosoma mansoni</option>
                        <option value="tetrahymena">Tetrahymena thermophila</option>
                        <option value="galdieria">Galdieria sulphuraria</option>
                        <option value="maize">Zea mays</option>
                        <option value="toxoplasma">Toxoplasma gondii</option>
                        <option value="caenorhabditis ">Caenorhabditis elegans</option>
                        <option value="aspergillus_fumigatus">Aspergillus fumigatus</option>
                        <option value="aspergillus_nidulans ">Aspergillus nidulans</option>
                        <option value="aspergillus_oryzae ">Aspergillus oryzae</option>
                        <option value="aspergillus_terreus">Aspergillus terreus</option>
                        <option value="botrytis_cinerea ">Botrytis cinerea</option>
                        <option value="candida_albicans ">Candida albicans</option>
                        <option value="candida_guilliermondii ">Candida guilliermondii</option>
                        <option value="candida_tropicalis ">Candida tropicalis</option>
                        <option value="chaetomium_globosum">Chaetomium globosum</option>
                        <option value="coccidioides_immitis">Coccidioides immitis</option>
                        <option value="coprinus">Coprinus cinereus</option>
                        <option value="coprinus_cinereus">Coprinus cinereus</option>
                        <option value="cryptococcus_neoformans_gattii">Cryptococcus neoformans gattii</option>
                        <option value="cryptococcus_neoformans_neoformans_B">Cryptococcus neoformans neoformans</option>
                        <option value="cryptococcus_neoformans_neoformans_JEC21">Cryptococcus neoformans neoformans</option>
                        <option value="cryptococcus">Cryptococcus neoformans</option>
                        <option value="debaryomyces_hansenii">Debaryomyces hansenii</option>
                        <option value="encephalitozoon_cuniculi_GB">Encephalitozoon cuniculi</option>
                        <option value="eremothecium_gossypii">Eremothecium gossypii</option>
                        <option value="fusarium_graminearum ">Fusarium graminearum</option>
                        <option value="histoplasma_capsulatum ">Histoplasma capsulatum</option>
                        <option value="histoplasma">Histoplasma capsulatum</option>
                        <option value="kluyveromyces_lactis ">Kluyveromyces lactis</option>
                        <option value="laccaria_bicolor ">Laccaria bicolor</option>
                        <option value="lamprey">Petromyzon marinus</option>
                        <option value="leishmania_tarentolae">Leishmania tarentolae</option>
                        <option value="lodderomyces_elongisporus">Lodderomyces elongisporus</option>
                        <option value="magnaporthe_grisea ">Magnaporthe grisea</option>
                        <option value="neurospora_crassa">Neurospora crassa</option>
                        <option value="phanerochaete_chrysosporium">Phanerochaete chrysosporium</option>
                        <option value="pichia_stipitis">Pichia stipitis</option>
                        <option value="rhizopus_oryzae">Rhizopus oryzae</option>
                        <option value="saccharomyces_cerevisiae_S288C">Saccharomyces cerevisiae</option>
                        <option value="saccharomyces_cerevisiae_rm11-1a_1">Saccharomyces cerevisiae</option>
                        <option value="saccharomyces">Saccharomyces cerevisiae</option>
                        <option value="schizosaccharomyces_pombe">Schizosaccharomyces pombe</option>
                        <option value="trichinella">Trichinella spiralis</option>
                        <option value="ustilago_maydis">Ustilago maydis</option>
                        <option value="yarrowia_lipolytica">Yarrowia lipolytica</option>
                        <option value="nasonia">Nasonia vitripennis</option>
                        <option value="tomato">Solanum lycopersicum</option>
                        <option value="chlamydomonas">Chlamydomonas reinhardtii</option>
                        <option value="amphimedon">Amphimedon queenslandica</option>
                        <option value="pneumocystis">Pneumocystis jirovecii</option>
                        <option value="chicken">Gallus gallus domesticus (chicken)</option>
                        <option value="cacao">Theobroma cacao (cacao)</option>
                        <option value="heliconius_melpomene1">Heliconius melpomene</option>
                        <option value="xenoturbella">Xenoturbella</option>
                        <option value="E_coli_K12">E coli K12</option>
                        <option value="c_elegans_trsk">c elegans trsk</option>
                        <option value="camponotus_floridanus">Camponotus floridanus</option>
                        <option value="coyote_tobacco">Coyote tobacco</option>
                        <option value="s_aureus">Staphylococcus aureus</option>
                        <option value="thermoanaerobacter_tengcongensis">Thermoanaerobacter tengcongensis</option>
                        <option value="wheat">wheat</option>
                        <option value="zebrafish">Danio rerio</option>
                        <option value="anidulans">Aspergillus nidulans</option>
                        <option value="bombus_impatiens1">Bombus impatiens1</option>
                        <option value="bombus_terrestris2">Bombus terrestris2</option>
                        <option value="botrytis_cinerea">Botrytis cinerea</option>
                        <option value="brugia_malayi">Brugia malayi</option>
                        <option value="conidiobolus_coronatus">Conidiobolus coronatus</option>
                        <option value="cryptococcus_neoformans">Cryptococcus neoformans</option>
                        <option value="culex_pipiens">Culex pipiens</option>
                        <option value="elephant_shark">Callorhinchus milii</option>
                        <option value="honeybee1">Apis mellifera</option>
                        <option value="phanerochaete_chrysosporium">Phanerochaete chrysosporium</option>
                        <option value="pea_aphid">Acyrthosiphon pisum</option>
                        <option value="rhodnius_prolixus">Rhodnius prolixus</option>
                        <option value="ustilago_maydis">Ustilago maydis</option>
                        <option value="verticillium_albo_atrum1">Verticillium albo atrum1</option>
                        <option value="verticillium_longisporum1">Verticillium longisporum1</option>
                        <option value="Xipophorus_maculatus">Xipophorus_maculatus</option>
                        <option value="adorsata">adorsata</option>
                        <option value="ancylostoma_ceylanicum">ancylostoma_ceylanicum</option>
                        <option value="maker2_athal1">maker2_athal1</option>
                        <option value="maker2_c_elegans1">maker2_c_elegans1</option>
                        <option value="maker2_dmel1">maker2_dmel1</option>
                        <option value="maker2_spomb1">maker2_spomb1</option>
                        <option value="parasteatoda">parasteatoda</option>
                        <option value="rice">rice</option>
                        <option value="schistosoma2">schistosoma2</option>
                        <option value="sulfolobus_solfataricus">sulfolobus_solfataricus</option>
                    </param>
                </when>
            </conditional>
            <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_path" value="arthropoda"/>
            <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_path" value="arthropoda"/>
            <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_path" value="arthropoda"/>
            <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>
        <test>
            <param name="input" value="genome.fa"/>
            <param name="lineage_path" value="arthropoda"/>
            <param name="mode" value="geno"/>
            <param name="adv|aug_prediction|augustus_mode" value="builtin"/>
            <param name="adv|aug_prediction|augustus_species" value="human"/>
            <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="genome.fa"/>
            <param name="lineage_path" value="arthropoda"/>
            <param name="mode" value="geno"/>
            <param name="adv|aug_prediction|augustus_mode" value="history"/>
            <param name="adv|aug_prediction|augustus_model" value="local.tar.gz" ftype="augustus"/>
            <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>
    </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>