bacterial_genome_annotation/main
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Tests Annotation of an assembled bacterial genomes to detect genes, potential plasmids, integrons and Insertion sequence (IS) elements.
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| Input sequence fasta | #main/Input sequence fasta | Can be any fasta file. |
|
| Select a AMRFinderPlus database | #main/Select a AMRFinderPlus database | Selecting this database is not necessary if the bacterial genome database (with Bakta) version is greater than 5.0. |
|
| Select a bacterial genome annotation database | #main/Select a bacterial genome annotation database | Select a database to predict CDS and small proteins (sORF) with Bakta. |
|
| Select a plasmid detection database | #main/Select a plasmid detection database | Select a database to identify plasmids with PlasmidFinder. |
|
Steps
| ID | Name | Description |
|---|---|---|
| 4 | genomic_annotation_insertionelement_isescan | genomic_annotation_insertionelement_isescan toolshed.g2.bx.psu.edu/repos/iuc/isescan/isescan/1.7.2.3+galaxy1 |
| 5 | genomic_annotation_integron | genomic_annotation_integron toolshed.g2.bx.psu.edu/repos/iuc/integron_finder/integron_finder/2.0.5+galaxy0 |
| 6 | genomic_annotation_plasmid_plasmidfinder | genomic_annotation_plasmid_plasmidfinder toolshed.g2.bx.psu.edu/repos/iuc/plasmidfinder/plasmidfinder/2.1.6+galaxy1 |
| 7 | Bakta | toolshed.g2.bx.psu.edu/repos/iuc/bakta/bakta/1.9.3+galaxy0 |
| 8 | ToolDistillator | ToolDistillator extracts results from tools and creates a JSON file for each tool toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator/tooldistillator/0.9+galaxy0 |
| 9 | ToolDistillator summarize | ToolDistillator summarize groups all JSON file into a unique JSON file toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator_summarize/tooldistillator_summarize/0.9+galaxy0 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| bakta_aminoacid_sequence_faa | #main/bakta_aminoacid_sequence_faa | n/a |
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| bakta_annotation_embl | #main/bakta_annotation_embl | n/a |
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| bakta_annotation_gbff | #main/bakta_annotation_gbff | n/a |
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| bakta_annotation_gff3 | #main/bakta_annotation_gff3 | n/a |
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| bakta_annotation_json | #main/bakta_annotation_json | n/a |
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| bakta_annotation_plot | #main/bakta_annotation_plot | n/a |
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| bakta_annotation_tabular | #main/bakta_annotation_tabular | n/a |
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| bakta_assembly_fasta | #main/bakta_assembly_fasta | n/a |
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| bakta_hypothetical_faa | #main/bakta_hypothetical_faa | n/a |
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| bakta_hypothetical_tabular | #main/bakta_hypothetical_tabular | n/a |
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| bakta_nucleotide_sequence_fasta | #main/bakta_nucleotide_sequence_fasta | n/a |
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| bakta_summary_text | #main/bakta_summary_text | n/a |
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| integronfinder2_logfile_text | #main/integronfinder2_logfile_text | n/a |
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| integronfinder2_results_tabular | #main/integronfinder2_results_tabular | n/a |
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| integronfinder2_summary | #main/integronfinder2_summary | n/a |
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| isescan_annotation_gff3 | #main/isescan_annotation_gff3 | n/a |
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| isescan_is_fasta | #main/isescan_is_fasta | n/a |
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| isescan_logfile_text | #main/isescan_logfile_text | n/a |
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| isescan_orf_faa | #main/isescan_orf_faa | n/a |
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| isescan_orf_fasta | #main/isescan_orf_fasta | n/a |
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| isescan_results_tabular | #main/isescan_results_tabular | n/a |
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| isescan_summary_tabular | #main/isescan_summary_tabular | n/a |
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| plasmidfinder_hit_genome_fasta | #main/plasmidfinder_hit_genome_fasta | n/a |
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| plasmidfinder_hit_reference_fasta | #main/plasmidfinder_hit_reference_fasta | n/a |
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| plasmidfinder_result_json | #main/plasmidfinder_result_json | n/a |
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| plasmidfinder_results_raw | #main/plasmidfinder_results_raw | n/a |
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| plasmidfinder_results_tabular | #main/plasmidfinder_results_tabular | n/a |
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| tooldistillator_results | #main/tooldistillator_results | n/a |
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| tooldistillator_summarize | #main/tooldistillator_summarize | n/a |
|
Version History
v1.1.2 (latest) Created 20th Jul 2024 at 03:02 by WorkflowHub Bot
Updated to v1.1.2
Frozen
v1.1.2082a807
v1.0 (earliest) Created 20th Jun 2024 at 03:02 by WorkflowHub Bot
Updated to v1.0
Frozen
v1.0
bb3655f
Creators and SubmitterActivity
Views: 816 Downloads: 224 Runs: 0
Created: 20th Jun 2024 at 03:01
AttributionsNone
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Teams: Intergalactic Workflow Commission (IWC), Vertebrate Genomes Pipelines in Galaxy, nf-core, iwc
Organizations: Bots, European Galaxy Team
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IWC - Intergalactic Workflow Commission
Space: This Team is not associated with a Space
Public web page: https://github.com/galaxyproject/iwc
