<tool id="socru" name="socru" version="@VERSION@">
    <description>Calculate the order and orientation of complete bacterial genomes</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="version_command" />
    <command detect_errors="exit_code"><![CDATA[
        #import re
        #import os.path
        
        #set $_input_file = re.sub(r'(\s|\(|\)|:|!)', '_', str($assembly.element_identifier))
        ln -s '${assembly}' $_input_file && 
        
        socru 

        --threads \${GALAXY_SLOTS:-4}
        
        --top_blast_hits top_blast_hits.tsv
        
        #if str($opt_args.max_bases_from_ends) != ""
            --max_bases_from_ends $opt_args.max_bases_from_ends
        #end if
        
        #if $opt_args.not_circular
            $opt_args.not_circular
        #end if

        --min_bit_score $opt_args.min_bit_score
        --min_alignment_length $opt_args.min_alignment_length

        #if $opt_args.verbose
            $opt_args.verbose
        #end if
        $species ${_input_file}
        > $output
    ]]></command>
    
    <inputs>
        <param name="assembly" type="data" format="fasta,fasta.gz" label="Select fasta dataset" help=""/>
        <param name="species" type="select" label="Select a species" >
            <option value="Acetobacter_ascendens">Acetobacter_ascendens</option>
            <option value="Acetobacter_pasteurianus">Acetobacter_pasteurianus</option>
            <option value="Achromobacter_denitrificans">Achromobacter_denitrificans</option>
            <option value="Achromobacter_insolitus">Achromobacter_insolitus</option>
            <option value="Achromobacter_spanius">Achromobacter_spanius</option>
            <option value="Achromobacter_xylosoxidans">Achromobacter_xylosoxidans</option>
            <option value="Acidipropionibacterium_acidipropionici">Acidipropionibacterium_acidipropionici</option>
            <option value="Acidipropionibacterium_jensenii">Acidipropionibacterium_jensenii</option>
            <option value="Acidovorax_carolinensis">Acidovorax_carolinensis</option>
            <option value="Acidovorax_sp.">Acidovorax_sp.</option>
            <option value="Acinetobacter_baumannii">Acinetobacter_baumannii</option>
            <option value="Acinetobacter_haemolyticus">Acinetobacter_haemolyticus</option>
            <option value="Acinetobacter_johnsonii">Acinetobacter_johnsonii</option>
            <option value="Acinetobacter_junii">Acinetobacter_junii</option>
            <option value="Acinetobacter_nosocomialis">Acinetobacter_nosocomialis</option>
            <option value="Acinetobacter_sp.">Acinetobacter_sp.</option>
            <option value="Actinoalloteichus_sp.">Actinoalloteichus_sp.</option>
            <option value="Actinobacillus_pleuropneumoniae">Actinobacillus_pleuropneumoniae</option>
            <option value="Actinomyces_sp.">Actinomyces_sp.</option>
            <option value="Actinoplanes_sp.">Actinoplanes_sp.</option>
            <option value="Aeromonas_caviae">Aeromonas_caviae</option>
            <option value="Aeromonas_hydrophila">Aeromonas_hydrophila</option>
            <option value="Aeromonas_salmonicida">Aeromonas_salmonicida</option>
            <option value="Aeromonas_sp.">Aeromonas_sp.</option>
            <option value="Aeromonas_veronii">Aeromonas_veronii</option>
            <option value="Aggregatibacter_actinomycetemcomitans">Aggregatibacter_actinomycetemcomitans</option>
            <option value="Aggregatibacter_aphrophilus">Aggregatibacter_aphrophilus</option>
            <option value="Agrobacterium_tumefaciens">Agrobacterium_tumefaciens</option>
            <option value="Akkermansia_muciniphila">Akkermansia_muciniphila</option>
            <option value="Alcaligenes_faecalis">Alcaligenes_faecalis</option>
            <option value="Alteromonas_macleodii">Alteromonas_macleodii</option>
            <option value="Alteromonas_mediterranea">Alteromonas_mediterranea</option>
            <option value="Alteromonas_sp.">Alteromonas_sp.</option>
            <option value="Alteromonas_stellipolaris">Alteromonas_stellipolaris</option>
            <option value="Amycolatopsis_mediterranei">Amycolatopsis_mediterranei</option>
            <option value="Anoxybacillus_flavithermus">Anoxybacillus_flavithermus</option>
            <option value="Aquimarina_sp.">Aquimarina_sp.</option>
            <option value="Arcobacter_butzleri">Arcobacter_butzleri</option>
            <option value="Arthrobacter_alpinus">Arthrobacter_alpinus</option>
            <option value="Arthrobacter_sp.">Arthrobacter_sp.</option>
            <option value="Azoarcus_sp.">Azoarcus_sp.</option>
            <option value="Azotobacter_vinelandii">Azotobacter_vinelandii</option>
            <option value="Bacillus_altitudinis">Bacillus_altitudinis</option>
            <option value="Bacillus_amyloliquefaciens">Bacillus_amyloliquefaciens</option>
            <option value="Bacillus_anthracis">Bacillus_anthracis</option>
            <option value="Bacillus_atrophaeus">Bacillus_atrophaeus</option>
            <option value="Bacillus_cellulasensis">Bacillus_cellulasensis</option>
            <option value="Bacillus_cereus">Bacillus_cereus</option>
            <option value="Bacillus_clausii">Bacillus_clausii</option>
            <option value="Bacillus_coagulans">Bacillus_coagulans</option>
            <option value="Bacillus_cytotoxicus">Bacillus_cytotoxicus</option>
            <option value="Bacillus_licheniformis">Bacillus_licheniformis</option>
            <option value="Bacillus_megaterium">Bacillus_megaterium</option>
            <option value="Bacillus_mycoides">Bacillus_mycoides</option>
            <option value="Bacillus_paralicheniformis">Bacillus_paralicheniformis</option>
            <option value="Bacillus_pumilus">Bacillus_pumilus</option>
            <option value="Bacillus_safensis">Bacillus_safensis</option>
            <option value="Bacillus_sp.">Bacillus_sp.</option>
            <option value="Bacillus_subtilis">Bacillus_subtilis</option>
            <option value="Bacillus_thuringiensis">Bacillus_thuringiensis</option>
            <option value="Bacillus_velezensis">Bacillus_velezensis</option>
            <option value="Bacteroides_fragilis">Bacteroides_fragilis</option>
            <option value="Bibersteinia_trehalosi">Bibersteinia_trehalosi</option>
            <option value="Bifidobacterium_adolescentis">Bifidobacterium_adolescentis</option>
            <option value="Bifidobacterium_bifidum">Bifidobacterium_bifidum</option>
            <option value="Bifidobacterium_breve">Bifidobacterium_breve</option>
            <option value="Bifidobacterium_longum">Bifidobacterium_longum</option>
            <option value="Bifidobacterium_pseudolongum">Bifidobacterium_pseudolongum</option>
            <option value="Blastochloris_viridis">Blastochloris_viridis</option>
            <option value="Bordetella_avium">Bordetella_avium</option>
            <option value="Bordetella_bronchiseptica">Bordetella_bronchiseptica</option>
            <option value="Bordetella_genomosp.">Bordetella_genomosp.</option>
            <option value="Bordetella_hinzii">Bordetella_hinzii</option>
            <option value="Bordetella_parapertussis">Bordetella_parapertussis</option>
            <option value="Bordetella_pertussis">Bordetella_pertussis</option>
            <option value="Bordetella_sp.">Bordetella_sp.</option>
            <option value="Bordetella_trematum">Bordetella_trematum</option>
            <option value="Brachybacterium_sp.">Brachybacterium_sp.</option>
            <option value="Brevibacillus_laterosporus">Brevibacillus_laterosporus</option>
            <option value="Brevibacterium_aurantiacum">Brevibacterium_aurantiacum</option>
            <option value="Brochothrix_thermosphacta">Brochothrix_thermosphacta</option>
            <option value="Burkholderia_ambifaria">Burkholderia_ambifaria</option>
            <option value="Burkholderia_cenocepacia">Burkholderia_cenocepacia</option>
            <option value="Burkholderia_gladioli">Burkholderia_gladioli</option>
            <option value="Burkholderia_sp.">Burkholderia_sp.</option>
            <option value="Burkholderia_ubonensis">Burkholderia_ubonensis</option>
            <option value="Burkholderia_vietnamiensis">Burkholderia_vietnamiensis</option>
            <option value="Calothrix_sp.">Calothrix_sp.</option>
            <option value="Campylobacter_coli">Campylobacter_coli</option>
            <option value="Campylobacter_concisus">Campylobacter_concisus</option>
            <option value="Campylobacter_fetus">Campylobacter_fetus</option>
            <option value="Campylobacter_iguaniorum">Campylobacter_iguaniorum</option>
            <option value="Campylobacter_insulaenigrae">Campylobacter_insulaenigrae</option>
            <option value="Campylobacter_jejuni">Campylobacter_jejuni</option>
            <option value="Campylobacter_lari">Campylobacter_lari</option>
            <option value="Campylobacter_sp.">Campylobacter_sp.</option>
            <option value="Candidatus_Arthromitus">Candidatus_Arthromitus</option>
            <option value="Candidatus_Kinetoplastibacterium">Candidatus_Kinetoplastibacterium</option>
            <option value="Candidatus_Liberibacter">Candidatus_Liberibacter</option>
            <option value="Capnocytophaga_canimorsus">Capnocytophaga_canimorsus</option>
            <option value="Capnocytophaga_sp.">Capnocytophaga_sp.</option>
            <option value="Capnocytophaga_sputigena">Capnocytophaga_sputigena</option>
            <option value="Cedecea_neteri">Cedecea_neteri</option>
            <option value="Cellulophaga_lytica">Cellulophaga_lytica</option>
            <option value="Chromobacterium_sp.">Chromobacterium_sp.</option>
            <option value="Chryseobacterium_indologenes">Chryseobacterium_indologenes</option>
            <option value="Chryseobacterium_shandongense">Chryseobacterium_shandongense</option>
            <option value="Chryseobacterium_sp.">Chryseobacterium_sp.</option>
            <option value="Citrobacter_amalonaticus">Citrobacter_amalonaticus</option>
            <option value="Citrobacter_freundii">Citrobacter_freundii</option>
            <option value="Citrobacter_koseri">Citrobacter_koseri</option>
            <option value="Citrobacter_sp.">Citrobacter_sp.</option>
            <option value="Citrobacter_werkmanii">Citrobacter_werkmanii</option>
            <option value="Clostridioides_difficile">Clostridioides_difficile</option>
            <option value="Clostridium_acetobutylicum">Clostridium_acetobutylicum</option>
            <option value="Clostridium_beijerinckii">Clostridium_beijerinckii</option>
            <option value="Clostridium_botulinum">Clostridium_botulinum</option>
            <option value="Clostridium_butyricum">Clostridium_butyricum</option>
            <option value="Clostridium_chauvoei">Clostridium_chauvoei</option>
            <option value="Clostridium_kluyveri">Clostridium_kluyveri</option>
            <option value="Clostridium_pasteurianum">Clostridium_pasteurianum</option>
            <option value="Clostridium_perfringens">Clostridium_perfringens</option>
            <option value="Clostridium_saccharobutylicum">Clostridium_saccharobutylicum</option>
            <option value="Clostridium_sp.">Clostridium_sp.</option>
            <option value="Clostridium_sporogenes">Clostridium_sporogenes</option>
            <option value="Collimonas_arenae">Collimonas_arenae</option>
            <option value="Colwellia_sp.">Colwellia_sp.</option>
            <option value="Corynebacterium_diphtheriae">Corynebacterium_diphtheriae</option>
            <option value="Corynebacterium_glutamicum">Corynebacterium_glutamicum</option>
            <option value="Corynebacterium_jeikeium">Corynebacterium_jeikeium</option>
            <option value="Corynebacterium_kutscheri">Corynebacterium_kutscheri</option>
            <option value="Corynebacterium_pseudotuberculosis">Corynebacterium_pseudotuberculosis</option>
            <option value="Corynebacterium_sp.">Corynebacterium_sp.</option>
            <option value="Corynebacterium_stationis">Corynebacterium_stationis</option>
            <option value="Corynebacterium_striatum">Corynebacterium_striatum</option>
            <option value="Corynebacterium_ulcerans">Corynebacterium_ulcerans</option>
            <option value="Corynebacterium_urealyticum">Corynebacterium_urealyticum</option>
            <option value="Cronobacter_sakazakii">Cronobacter_sakazakii</option>
            <option value="Cupriavidus_necator">Cupriavidus_necator</option>
            <option value="Cupriavidus_sp.">Cupriavidus_sp.</option>
            <option value="Cutibacterium_acnes">Cutibacterium_acnes</option>
            <option value="Desulfovibrio_vulgaris">Desulfovibrio_vulgaris</option>
            <option value="Dickeya_solani">Dickeya_solani</option>
            <option value="Dickeya_zeae">Dickeya_zeae</option>
            <option value="Dokdonia_sp.">Dokdonia_sp.</option>
            <option value="Edwardsiella_ictaluri">Edwardsiella_ictaluri</option>
            <option value="Edwardsiella_tarda">Edwardsiella_tarda</option>
            <option value="Elizabethkingia_anophelis">Elizabethkingia_anophelis</option>
            <option value="Elizabethkingia_meningoseptica">Elizabethkingia_meningoseptica</option>
            <option value="Enterobacter_asburiae">Enterobacter_asburiae</option>
            <option value="Enterobacter_cloacae">Enterobacter_cloacae</option>
            <option value="Enterobacter_hormaechei">Enterobacter_hormaechei</option>
            <option value="Enterobacter_roggenkampii">Enterobacter_roggenkampii</option>
            <option value="Enterobacter_sp.">Enterobacter_sp.</option>
            <option value="Enterobacteriaceae_bacterium">Enterobacteriaceae_bacterium</option>
            <option value="Enterococcus_durans">Enterococcus_durans</option>
            <option value="Enterococcus_faecalis">Enterococcus_faecalis</option>
            <option value="Enterococcus_faecium">Enterococcus_faecium</option>
            <option value="Enterococcus_hirae">Enterococcus_hirae</option>
            <option value="Enterococcus_mundtii">Enterococcus_mundtii</option>
            <option value="Enterococcus_sp.">Enterococcus_sp.</option>
            <option value="Erwinia_amylovora">Erwinia_amylovora</option>
            <option value="Erysipelothrix_rhusiopathiae">Erysipelothrix_rhusiopathiae</option>
            <option value="Erysipelotrichaceae_bacterium">Erysipelotrichaceae_bacterium</option>
            <option value="Escherichia_albertii">Escherichia_albertii</option>
            <option value="Escherichia_coli">Escherichia_coli</option>
            <option value="Ethanoligenens_harbinense">Ethanoligenens_harbinense</option>
            <option value="Exiguobacterium_sp.">Exiguobacterium_sp.</option>
            <option value="Faecalibacterium_prausnitzii">Faecalibacterium_prausnitzii</option>
            <option value="Flavobacterium_columnare">Flavobacterium_columnare</option>
            <option value="Flavobacterium_psychrophilum">Flavobacterium_psychrophilum</option>
            <option value="Flavobacterium_sp.">Flavobacterium_sp.</option>
            <option value="Francisella_philomiragia">Francisella_philomiragia</option>
            <option value="Francisella_sp.">Francisella_sp.</option>
            <option value="Francisella_tularensis">Francisella_tularensis</option>
            <option value="Fusobacterium_hwasookii">Fusobacterium_hwasookii</option>
            <option value="Fusobacterium_necrophorum">Fusobacterium_necrophorum</option>
            <option value="Fusobacterium_nucleatum">Fusobacterium_nucleatum</option>
            <option value="Fusobacterium_periodonticum">Fusobacterium_periodonticum</option>
            <option value="Fusobacterium_varium">Fusobacterium_varium</option>
            <option value="Geobacillus_sp.">Geobacillus_sp.</option>
            <option value="Geobacillus_thermodenitrificans">Geobacillus_thermodenitrificans</option>
            <option value="Geobacillus_thermoleovorans">Geobacillus_thermoleovorans</option>
            <option value="Glaesserella_parasuis">Glaesserella_parasuis</option>
            <option value="Gluconobacter_oxydans">Gluconobacter_oxydans</option>
            <option value="Gordonia_sp.">Gordonia_sp.</option>
            <option value="Granulibacter_bethesdensis">Granulibacter_bethesdensis</option>
            <option value="Haemophilus_haemolyticus">Haemophilus_haemolyticus</option>
            <option value="Haemophilus_influenzae">Haemophilus_influenzae</option>
            <option value="Haemophilus_parainfluenzae">Haemophilus_parainfluenzae</option>
            <option value="Hafnia_alvei">Hafnia_alvei</option>
            <option value="Halomonas_sp.">Halomonas_sp.</option>
            <option value="Herbaspirillum_seropedicae">Herbaspirillum_seropedicae</option>
            <option value="Histophilus_somni">Histophilus_somni</option>
            <option value="Hungateiclostridium_thermocellum">Hungateiclostridium_thermocellum</option>
            <option value="Hymenobacter_sp.">Hymenobacter_sp.</option>
            <option value="Jonesia_denitrificans">Jonesia_denitrificans</option>
            <option value="Ketogulonicigenium_vulgare">Ketogulonicigenium_vulgare</option>
            <option value="Klebsiella_aerogenes">Klebsiella_aerogenes</option>
            <option value="Klebsiella_michiganensis">Klebsiella_michiganensis</option>
            <option value="Klebsiella_oxytoca">Klebsiella_oxytoca</option>
            <option value="Klebsiella_pneumoniae">Klebsiella_pneumoniae</option>
            <option value="Klebsiella_quasipneumoniae">Klebsiella_quasipneumoniae</option>
            <option value="Klebsiella_sp.">Klebsiella_sp.</option>
            <option value="Klebsiella_variicola">Klebsiella_variicola</option>
            <option value="Lachnospiraceae_bacterium">Lachnospiraceae_bacterium</option>
            <option value="Lactobacillus_acidophilus">Lactobacillus_acidophilus</option>
            <option value="Lactobacillus_amylovorus">Lactobacillus_amylovorus</option>
            <option value="Lactobacillus_backii">Lactobacillus_backii</option>
            <option value="Lactobacillus_brevis">Lactobacillus_brevis</option>
            <option value="Lactobacillus_casei">Lactobacillus_casei</option>
            <option value="Lactobacillus_curvatus">Lactobacillus_curvatus</option>
            <option value="Lactobacillus_delbrueckii">Lactobacillus_delbrueckii</option>
            <option value="Lactobacillus_fermentum">Lactobacillus_fermentum</option>
            <option value="Lactobacillus_gasseri">Lactobacillus_gasseri</option>
            <option value="Lactobacillus_helveticus">Lactobacillus_helveticus</option>
            <option value="Lactobacillus_johnsonii">Lactobacillus_johnsonii</option>
            <option value="Lactobacillus_paracasei">Lactobacillus_paracasei</option>
            <option value="Lactobacillus_paracollinoides">Lactobacillus_paracollinoides</option>
            <option value="Lactobacillus_pentosus">Lactobacillus_pentosus</option>
            <option value="Lactobacillus_plantarum">Lactobacillus_plantarum</option>
            <option value="Lactobacillus_reuteri">Lactobacillus_reuteri</option>
            <option value="Lactobacillus_rhamnosus">Lactobacillus_rhamnosus</option>
            <option value="Lactobacillus_sakei">Lactobacillus_sakei</option>
            <option value="Lactobacillus_salivarius">Lactobacillus_salivarius</option>
            <option value="Lactobacillus_sp.">Lactobacillus_sp.</option>
            <option value="Lactococcus_garvieae">Lactococcus_garvieae</option>
            <option value="Lactococcus_lactis">Lactococcus_lactis</option>
            <option value="Legionella_longbeachae">Legionella_longbeachae</option>
            <option value="Legionella_pneumophila">Legionella_pneumophila</option>
            <option value="Legionella_sainthelensi">Legionella_sainthelensi</option>
            <option value="Lelliottia_amnigena">Lelliottia_amnigena</option>
            <option value="Leptolyngbya_boryana">Leptolyngbya_boryana</option>
            <option value="Leptotrichia_sp.">Leptotrichia_sp.</option>
            <option value="Leuconostoc_gelidum">Leuconostoc_gelidum</option>
            <option value="Leuconostoc_mesenteroides">Leuconostoc_mesenteroides</option>
            <option value="Listeria_ivanovii">Listeria_ivanovii</option>
            <option value="Listeria_monocytogenes">Listeria_monocytogenes</option>
            <option value="Lysinibacillus_sphaericus">Lysinibacillus_sphaericus</option>
            <option value="Mannheimia_haemolytica">Mannheimia_haemolytica</option>
            <option value="Mannheimia_varigena">Mannheimia_varigena</option>
            <option value="Marinobacter_sp.">Marinobacter_sp.</option>
            <option value="Massilia_sp.">Massilia_sp.</option>
            <option value="Megasphaera_elsdenii">Megasphaera_elsdenii</option>
            <option value="Melissococcus_plutonius">Melissococcus_plutonius</option>
            <option value="Methylobacterium_sp.">Methylobacterium_sp.</option>
            <option value="Methylorubrum_extorquens">Methylorubrum_extorquens</option>
            <option value="Moraxella_bovoculi">Moraxella_bovoculi</option>
            <option value="Moraxella_catarrhalis">Moraxella_catarrhalis</option>
            <option value="Moraxella_osloensis">Moraxella_osloensis</option>
            <option value="Morganella_morganii">Morganella_morganii</option>
            <option value="Mucilaginibacter_sp.">Mucilaginibacter_sp.</option>
            <option value="Neisseria_elongata">Neisseria_elongata</option>
            <option value="Neisseria_gonorrhoeae">Neisseria_gonorrhoeae</option>
            <option value="Neisseria_lactamica">Neisseria_lactamica</option>
            <option value="Neisseria_meningitidis">Neisseria_meningitidis</option>
            <option value="Neisseria_sp.">Neisseria_sp.</option>
            <option value="Nocardia_farcinica">Nocardia_farcinica</option>
            <option value="Nocardiopsis_dassonvillei">Nocardiopsis_dassonvillei</option>
            <option value="Nonlabens_sp.">Nonlabens_sp.</option>
            <option value="Nostoc_sp.">Nostoc_sp.</option>
            <option value="Novosphingobium_sp.">Novosphingobium_sp.</option>
            <option value="Oblitimonas_alkaliphila">Oblitimonas_alkaliphila</option>
            <option value="Paenibacillus_larvae">Paenibacillus_larvae</option>
            <option value="Paenibacillus_mucilaginosus">Paenibacillus_mucilaginosus</option>
            <option value="Paenibacillus_polymyxa">Paenibacillus_polymyxa</option>
            <option value="Paenibacillus_sp.">Paenibacillus_sp.</option>
            <option value="Pandoraea_apista">Pandoraea_apista</option>
            <option value="Pandoraea_pnomenusa">Pandoraea_pnomenusa</option>
            <option value="Pantoea_agglomerans">Pantoea_agglomerans</option>
            <option value="Pantoea_ananatis">Pantoea_ananatis</option>
            <option value="Pantoea_sp.">Pantoea_sp.</option>
            <option value="Pantoea_vagans">Pantoea_vagans</option>
            <option value="Paraburkholderia_caribensis">Paraburkholderia_caribensis</option>
            <option value="Paracoccus_yeei">Paracoccus_yeei</option>
            <option value="Parageobacillus_thermoglucosidasius">Parageobacillus_thermoglucosidasius</option>
            <option value="Parvimonas_micra">Parvimonas_micra</option>
            <option value="Pasteurella_multocida">Pasteurella_multocida</option>
            <option value="Pectobacterium_atrosepticum">Pectobacterium_atrosepticum</option>
            <option value="Pectobacterium_carotovorum">Pectobacterium_carotovorum</option>
            <option value="Pectobacterium_parmentieri">Pectobacterium_parmentieri</option>
            <option value="Pediococcus_acidilactici">Pediococcus_acidilactici</option>
            <option value="Pediococcus_claussenii">Pediococcus_claussenii</option>
            <option value="Pediococcus_damnosus">Pediococcus_damnosus</option>
            <option value="Pediococcus_pentosaceus">Pediococcus_pentosaceus</option>
            <option value="Phaeobacter_gallaeciensis">Phaeobacter_gallaeciensis</option>
            <option value="Phaeobacter_inhibens">Phaeobacter_inhibens</option>
            <option value="Phaeobacter_piscinae">Phaeobacter_piscinae</option>
            <option value="Photobacterium_damselae">Photobacterium_damselae</option>
            <option value="Photorhabdus_laumondii">Photorhabdus_laumondii</option>
            <option value="Piscirickettsia_salmonis">Piscirickettsia_salmonis</option>
            <option value="Planococcus_sp.">Planococcus_sp.</option>
            <option value="Plantactinospora_sp.">Plantactinospora_sp.</option>
            <option value="Porphyromonas_gingivalis">Porphyromonas_gingivalis</option>
            <option value="Proteus_mirabilis">Proteus_mirabilis</option>
            <option value="Providencia_rettgeri">Providencia_rettgeri</option>
            <option value="Providencia_stuartii">Providencia_stuartii</option>
            <option value="Pseudoalteromonas_luteoviolacea">Pseudoalteromonas_luteoviolacea</option>
            <option value="Pseudoalteromonas_piscicida">Pseudoalteromonas_piscicida</option>
            <option value="Pseudoalteromonas_sp.">Pseudoalteromonas_sp.</option>
            <option value="Pseudomonas_aeruginosa">Pseudomonas_aeruginosa</option>
            <option value="Pseudomonas_brassicacearum">Pseudomonas_brassicacearum</option>
            <option value="Pseudomonas_chlororaphis">Pseudomonas_chlororaphis</option>
            <option value="Pseudomonas_entomophila">Pseudomonas_entomophila</option>
            <option value="Pseudomonas_fluorescens">Pseudomonas_fluorescens</option>
            <option value="Pseudomonas_frederiksbergensis">Pseudomonas_frederiksbergensis</option>
            <option value="Pseudomonas_koreensis">Pseudomonas_koreensis</option>
            <option value="Pseudomonas_mendocina">Pseudomonas_mendocina</option>
            <option value="Pseudomonas_monteilii">Pseudomonas_monteilii</option>
            <option value="Pseudomonas_orientalis">Pseudomonas_orientalis</option>
            <option value="Pseudomonas_parafulva">Pseudomonas_parafulva</option>
            <option value="Pseudomonas_protegens">Pseudomonas_protegens</option>
            <option value="Pseudomonas_putida">Pseudomonas_putida</option>
            <option value="Pseudomonas_sp.">Pseudomonas_sp.</option>
            <option value="Pseudomonas_stutzeri">Pseudomonas_stutzeri</option>
            <option value="Pseudomonas_synxantha">Pseudomonas_synxantha</option>
            <option value="Pseudomonas_syringae">Pseudomonas_syringae</option>
            <option value="Pseudonocardia_sp.">Pseudonocardia_sp.</option>
            <option value="Psychrobacter_sp.">Psychrobacter_sp.</option>
            <option value="Rahnella_aquatilis">Rahnella_aquatilis</option>
            <option value="Ralstonia_pickettii">Ralstonia_pickettii</option>
            <option value="Raoultella_ornithinolytica">Raoultella_ornithinolytica</option>
            <option value="Rhizobium_etli">Rhizobium_etli</option>
            <option value="Rhizobium_leguminosarum">Rhizobium_leguminosarum</option>
            <option value="Rhizobium_phaseoli">Rhizobium_phaseoli</option>
            <option value="Rhizobium_sp.">Rhizobium_sp.</option>
            <option value="Rhodobacter_sphaeroides">Rhodobacter_sphaeroides</option>
            <option value="Rhodococcus_opacus">Rhodococcus_opacus</option>
            <option value="Rhodococcus_ruber">Rhodococcus_ruber</option>
            <option value="Rhodococcus_sp.">Rhodococcus_sp.</option>
            <option value="Rhodovulum_sulfidophilum">Rhodovulum_sulfidophilum</option>
            <option value="Riemerella_anatipestifer">Riemerella_anatipestifer</option>
            <option value="Ruegeria_sp.">Ruegeria_sp.</option>
            <option value="Salmonella_bongori">Salmonella_bongori</option>
            <option value="Salmonella_enterica">Salmonella_enterica</option>
            <option value="Selenomonas_sp.">Selenomonas_sp.</option>
            <option value="Serratia_fonticola">Serratia_fonticola</option>
            <option value="Serratia_liquefaciens">Serratia_liquefaciens</option>
            <option value="Serratia_marcescens">Serratia_marcescens</option>
            <option value="Serratia_plymuthica">Serratia_plymuthica</option>
            <option value="Serratia_rubidaea">Serratia_rubidaea</option>
            <option value="Serratia_sp.">Serratia_sp.</option>
            <option value="Shewanella_baltica">Shewanella_baltica</option>
            <option value="Shewanella_putrefaciens">Shewanella_putrefaciens</option>
            <option value="Shewanella_sp.">Shewanella_sp.</option>
            <option value="Shimwellia_blattae">Shimwellia_blattae</option>
            <option value="Sinorhizobium_fredii">Sinorhizobium_fredii</option>
            <option value="Sinorhizobium_meliloti">Sinorhizobium_meliloti</option>
            <option value="Sorangium_cellulosum">Sorangium_cellulosum</option>
            <option value="Sphingobacterium_sp.">Sphingobacterium_sp.</option>
            <option value="Sphingobium_yanoikuyae">Sphingobium_yanoikuyae</option>
            <option value="Sporosarcina_sp.">Sporosarcina_sp.</option>
            <option value="Sporosarcina_ureae">Sporosarcina_ureae</option>
            <option value="Staphylococcus_argenteus">Staphylococcus_argenteus</option>
            <option value="Staphylococcus_aureus">Staphylococcus_aureus</option>
            <option value="Staphylococcus_capitis">Staphylococcus_capitis</option>
            <option value="Staphylococcus_caprae">Staphylococcus_caprae</option>
            <option value="Staphylococcus_condimenti">Staphylococcus_condimenti</option>
            <option value="Staphylococcus_epidermidis">Staphylococcus_epidermidis</option>
            <option value="Staphylococcus_equorum">Staphylococcus_equorum</option>
            <option value="Staphylococcus_haemolyticus">Staphylococcus_haemolyticus</option>
            <option value="Staphylococcus_hyicus">Staphylococcus_hyicus</option>
            <option value="Staphylococcus_lugdunensis">Staphylococcus_lugdunensis</option>
            <option value="Staphylococcus_nepalensis">Staphylococcus_nepalensis</option>
            <option value="Staphylococcus_pseudintermedius">Staphylococcus_pseudintermedius</option>
            <option value="Staphylococcus_saprophyticus">Staphylococcus_saprophyticus</option>
            <option value="Staphylococcus_schleiferi">Staphylococcus_schleiferi</option>
            <option value="Staphylococcus_simulans">Staphylococcus_simulans</option>
            <option value="Staphylococcus_sp.">Staphylococcus_sp.</option>
            <option value="Staphylococcus_warneri">Staphylococcus_warneri</option>
            <option value="Staphylococcus_xylosus">Staphylococcus_xylosus</option>
            <option value="Stenotrophomonas_maltophilia">Stenotrophomonas_maltophilia</option>
            <option value="Stenotrophomonas_sp.">Stenotrophomonas_sp.</option>
            <option value="Streptococcus_agalactiae">Streptococcus_agalactiae</option>
            <option value="Streptococcus_anginosus">Streptococcus_anginosus</option>
            <option value="Streptococcus_constellatus">Streptococcus_constellatus</option>
            <option value="Streptococcus_cristatus">Streptococcus_cristatus</option>
            <option value="Streptococcus_dysgalactiae">Streptococcus_dysgalactiae</option>
            <option value="Streptococcus_equi">Streptococcus_equi</option>
            <option value="Streptococcus_equinus">Streptococcus_equinus</option>
            <option value="Streptococcus_gallolyticus">Streptococcus_gallolyticus</option>
            <option value="Streptococcus_gordonii">Streptococcus_gordonii</option>
            <option value="Streptococcus_iniae">Streptococcus_iniae</option>
            <option value="Streptococcus_intermedius">Streptococcus_intermedius</option>
            <option value="Streptococcus_lutetiensis">Streptococcus_lutetiensis</option>
            <option value="Streptococcus_mitis">Streptococcus_mitis</option>
            <option value="Streptococcus_mutans">Streptococcus_mutans</option>
            <option value="Streptococcus_oralis">Streptococcus_oralis</option>
            <option value="Streptococcus_pneumoniae">Streptococcus_pneumoniae</option>
            <option value="Streptococcus_pyogenes">Streptococcus_pyogenes</option>
            <option value="Streptococcus_salivarius">Streptococcus_salivarius</option>
            <option value="Streptococcus_sanguinis">Streptococcus_sanguinis</option>
            <option value="Streptococcus_sobrinus">Streptococcus_sobrinus</option>
            <option value="Streptococcus_sp.">Streptococcus_sp.</option>
            <option value="Streptococcus_suis">Streptococcus_suis</option>
            <option value="Streptococcus_thermophilus">Streptococcus_thermophilus</option>
            <option value="Streptococcus_uberis">Streptococcus_uberis</option>
            <option value="Streptomyces_albulus">Streptomyces_albulus</option>
            <option value="Streptomyces_albus">Streptomyces_albus</option>
            <option value="Streptomyces_hygroscopicus">Streptomyces_hygroscopicus</option>
            <option value="Streptomyces_lydicus">Streptomyces_lydicus</option>
            <option value="Streptomyces_sp.">Streptomyces_sp.</option>
            <option value="Streptomyces_venezuelae">Streptomyces_venezuelae</option>
            <option value="Sulfurospirillum_sp.">Sulfurospirillum_sp.</option>
            <option value="Tatlockia_micdadei">Tatlockia_micdadei</option>
            <option value="Taylorella_equigenitalis">Taylorella_equigenitalis</option>
            <option value="Tetragenococcus_halophilus">Tetragenococcus_halophilus</option>
            <option value="Thalassolituus_oleivorans">Thalassolituus_oleivorans</option>
            <option value="Thermoclostridium_stercorarium">Thermoclostridium_stercorarium</option>
            <option value="Veillonella_parvula">Veillonella_parvula</option>
            <option value="Vibrio_alginolyticus">Vibrio_alginolyticus</option>
            <option value="Vibrio_anguillarum">Vibrio_anguillarum</option>
            <option value="Vibrio_campbellii">Vibrio_campbellii</option>
            <option value="Vibrio_cholerae">Vibrio_cholerae</option>
            <option value="Vibrio_coralliilyticus">Vibrio_coralliilyticus</option>
            <option value="Vibrio_diabolicus">Vibrio_diabolicus</option>
            <option value="Vibrio_fluvialis">Vibrio_fluvialis</option>
            <option value="Vibrio_harveyi">Vibrio_harveyi</option>
            <option value="Vibrio_natriegens">Vibrio_natriegens</option>
            <option value="Vibrio_owensii">Vibrio_owensii</option>
            <option value="Vibrio_parahaemolyticus">Vibrio_parahaemolyticus</option>
            <option value="Vibrio_sp.">Vibrio_sp.</option>
            <option value="Vibrio_vulnificus">Vibrio_vulnificus</option>
            <option value="Virgibacillus_sp.">Virgibacillus_sp.</option>
            <option value="Weissella_ceti">Weissella_ceti</option>
            <option value="Weissella_cibaria">Weissella_cibaria</option>
            <option value="Yersinia_enterocolitica">Yersinia_enterocolitica</option>
            <option value="Yersinia_frederiksenii">Yersinia_frederiksenii</option>
            <option value="Yersinia_intermedia">Yersinia_intermedia</option>
            <option value="Yersinia_pestis">Yersinia_pestis</option>
            <option value="Yersinia_pseudotuberculosis">Yersinia_pseudotuberculosis</option>
            <option value="Yersinia_ruckeri">Yersinia_ruckeri</option>
            <option value="Zymomonas_mobilis">Zymomonas_mobilis</option>
        </param> 
        <section name="opt_args" title="Optional Arguments">
        <param argument="--max_bases_from_ends" type="integer" value="" optional="True" label="Only look at this number of bases from start and end of fragment" help="Take this number of bases from the start and end of a fragment and compare to the database. This is an experimental feature, it hasn't performed as expected and may be removed at a later point. (default: None)" />
        <param argument="--min_bit_score" type="integer" value="100" label="Minimum bit score" help="Internally blastn is used and this allows you to specify the minimum bit score for a hit to be considered, since blast will throw up a lot of small hits (default: 100)" />
        <param argument="--min_alignment_length" type="integer" value="100" label="Minimum alignment length " help="Only consider blast alignment lengths above this value. Remember that there can be some very short fragments between rrns, so you'll need to know the approximate minimum fragment size (in bases) before increasing this value too high. (default: 100)" />
        <param argument="--not_circular" type="boolean" truevalue="--not_circular" falsevalue="" checked="false" label="Assume chromosome is not circularised" help="(default: False)" />
        <param argument="--verbose" type="boolean" truevalue="--verbose" falsevalue="" checked="false" label="Turn on debugging" help="(Default:No)" />
        </section>
    </inputs>

    <outputs>
        <data name="novel_profiles" format="tabular" label="${tool.name} on ${on_string}: Novel profiles" from_work_dir="profile.txt.novel"/>
        <data name="new_fragments" format="fasta" label="${tool.name} on ${on_string}: New fragments" from_work_dir="novel_fragments.fa"/>
        <data name="top_blast_hits" format="tabular" label="${tool.name} on ${on_string}: Top blast hits" from_work_dir="top_blast_hits.tsv"/>      
        <data name="output" format="tabular" label="${tool.name} on ${on_string}: Output"/>
        <data name="plot" format="pdf" label="${tool.name} on ${on_string}: Plot" from_work_dir="genome_structure.pdf"/>
    </outputs>

    <tests>
        <test>
        <param name="assembly" value="test.fa" ftype="fasta" />
        <param name="species" value="Salmonella_enterica"/>
        <output name="output" ftype="tabular" file="output.txt" compare="contains" />
        </test>
    </tests>

    <help><![CDATA[
    usage: socru [options] species assembly.fasta

    Order and orientation of complete bacterial genomes
    
    Documentation can be found at `<https://github.com/quadram-institute-bioscience/socru>`_.
    ]]></help>
 <expand macro="citations" />
</tool>