annotate socru.xml @ 0:ce0c9fe32e04 draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/socru commit 6fbcf349a029961f0f45eaf11ade1fbceba42ac1"

<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
        
        $opt_args.not_circular

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

        '$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)" />
        </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[
    Socru allows you to easily identify and communicate the order and orientation
    of complete genomes around ribosomal operons.
    
    These large scale structural variants have real impacts on the phenotype of the organism,
    and with the advent of long read sequencing, we can now start to delve into the mechanisms at work.
   
    Documentation can be found at `<https://github.com/quadram-institute-bioscience/socru>`_.
    ]]></help>
    <expand macro="citations" />
</tool>