| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/bakta/bakta/1.9.3+galaxy0 (this tool) |
| toolshed.g2.bx.psu.edu/repos/iuc/bakta/bakta/1.9.2+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/iuc/bakta/bakta/1.8.2+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/iuc/bakta/bakta/1.8.1+galaxy1 |
| toolshed.g2.bx.psu.edu/repos/iuc/bakta/bakta/1.6.1+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/iuc/bakta/bakta/1.5.0+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/iuc/bakta/bakta/1.4.2+galaxy0 |
| bakta |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| bakta | 1.9.3 | package |
| Additional information about this tool |
mkdir -p ./database_path/amrfinderplus-db &&
ln -s '$(input_option.bakta_db_select.fields.path)'/* database_path &&
ln -s '$(input_option.amrfinder_db_select.fields.path)/' database_path/amrfinderplus-db/latest &&
bakta
--verbose
#*======================================
CPU option
======================================*#
--threads \${GALAXY_SLOTS:-1}
#*======================================
Bakta database
======================================*#
--db './database_path'
--output 'bakta_output'
#if $input_option.min_contig_length
--min-contig-length $input_option.min_contig_length
#else if $annotation.compliant
--min-contig-length 200
#else
--min-contig-length 1
#end if
--prefix bakta_output
#*======================================
Organism options
genus/species/strain/plasmid
======================================*#
#if $organism.genus
--genus '$organism.genus'
#end if
#if $organism.species
--species '$organism.species'
#end if
#if $organism.strain
--strain '$organism.strain'
#end if
#if $organism.plasmid
--plasmid '$organism.plasmid'
#end if
#*======================================
Annotation options
gram type, prodigal/protein file
======================================*#
$annotation.complete
#if $annotation.prodigal
--prodigal-tf '$annotation.prodigal'
#end if
#if $annotation.translation_table
--translation-table '$annotation.translation_table'
#end if
--gram '?'
$annotation.keep_contig_headers
#if $annotation.replicons
--replicons '$annotation.replicons'
#end if
$annotation.compliant
#if $annotation.proteins
--proteins '$annotation.proteins'
#end if
#if $annotation.regions
--regions '$annotation.regions'
#end if
#*======================================
Workflow OPTIONS
skip some step of the bakta analysis
======================================*#
#echo " ".join($workflow.skip_analysis)
#*======================================
Genome file
======================================*#
'$input_option.input_file'
#*======================================
LOG file
======================================*#
| tee '$logfile'
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
input_option|input_file: NC_002127.1.fna input_option|min_contig_length: 250 input_option|bakta_db_select: V5.1_light_2024-01-19 input_option|amrfinder_db_select: V3.12-2024-05-02.2 output_files|output_selection: ['file_tsv', 'file_gff3', 'file_gbff', 'file_embl', 'file_fna', 'file_ffn', 'file_faa', 'hypo_tsv', 'hypo_fa', 'sum_txt', 'file_json', 'file_plot', 'log_txt'] |
name: value name: value name: value name: value name: value name: value name: value name: value name: value name: value name: value name: value name: value |
NC_002127.1.fna value |
| Test-2 |
input_option|input_file: NC_002127.1.fna input_option|min_contig_length: 250 input_option|bakta_db_select: V5.1_light_2024-01-19 input_option|amrfinder_db_select: V3.12-2024-05-02.2 organism|genus: Escherichia organism|species: coli O157:H7 organism|strain: Sakai organism|plasmid: pOSAK1 annotation|keep_contig_headers: True workflow|skip_analysis: ['--skip-trna', '--skip-tmrna'] |
name: value name: value name: value name: value |
NC_002127.1.fna value |
| Test-3 |
input_option|input_file: NC_002127.1.fna input_option|min_contig_length: 350 input_option|bakta_db_select: V5.0_2022-08-19 input_option|amrfinder_db_select: V3.12-2024-05-02.2 workflow|skip_analysis: ['--skip-trna', '--skip-tmrna', '--skip-rrna', '--skip-ncrna', '--skip-ncrna-region', '--skip-crispr', '--skip-cds', '--skip-sorf', '--skip-gap', '--skip-ori', '--skip-plot'] |
name: value name: value name: value |
NC_002127.1.fna value |
| Test-4 |
input_option|input_file: NC_002127.1.fna input_option|bakta_db_select: V5.1_light_2024-01-19 input_option|amrfinder_db_select: V3.12-2024-05-02.2 annotation|complete: True annotation|prodigal: prodigal.tf annotation|translation_table: 4 annotation|replicons: replicons.tsv annotation|compliant: True annotation|proteins: user-proteins.faa |
name: value name: value name: value name: value |
NC_002127.1.fna prodigal.tf replicons.tsv user-proteins.faa value |
| Test-5 |
input_option|input_file: NC_002127.1.fna input_option|bakta_db_select: V5.1_light_2024-01-19 input_option|amrfinder_db_select: V3.12-2024-05-02.2 annotation|complete: True annotation|translation_table: 4 workflow|skip_analysis: ['--skip-trna', '--skip-tmrna', '--skip-rrna', '--skip-ncrna', '--skip-ncrna-region', '--skip-crispr', '--skip-cds', '--skip-sorf', '--skip-gap', '--skip-ori', '--skip-plot'] output_files|output_selection: ['log_txt', 'sum_txt'] |
name: value name: value |
NC_002127.1.fna value |
| Test-6 |
input_option|input_file: NC_002127.1.fna input_option|bakta_db_select: V5.1_light_2024-01-19 input_option|amrfinder_db_select: V3.12-2024-05-02.2 annotation|meta: True output_files|output_selection: ['file_tsv', 'file_gff3', 'file_gbff', 'file_embl', 'file_fna', 'file_ffn', 'file_faa', 'hypo_tsv', 'hypo_fa', 'sum_txt', 'file_json', 'file_plot', 'log_txt'] |
name: value name: value name: value name: value name: value name: value name: value name: value name: value name: value name: value name: value name: value |
NC_002127.1.fna value |