amr_gene_detection/main
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Workflow Type: Galaxy
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Tests Antimicrobial resistance gene detection from assembled bacterial genomes
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| Input sequence fasta | #main/Input sequence fasta | Can be any fasta file. |
|
| Select a AMR genes detection database | #main/Select a AMR genes detection database | Select the database to identify AMR genes with AMRFinderPlus. |
|
| Select a taxonomy group point mutation | #main/Select a taxonomy group point mutation | Select the database to identify resistance-associated point mutations with AMRFinderPlus. |
|
| Select a virulence genes detection database | #main/Select a virulence genes detection database | Select the database to identify virulence genes with ABRicate.. |
|
Steps
| ID | Name | Description |
|---|---|---|
| 4 | staramr_amr_genes | staramr_amr_genes toolshed.g2.bx.psu.edu/repos/nml/staramr/staramr_search/0.10.0+galaxy1 |
| 5 | amrfinderplus_point_mutation | amrfinderplus_point_mutation toolshed.g2.bx.psu.edu/repos/iuc/amrfinderplus/amrfinderplus/3.12.8+galaxy0 |
| 6 | abricate_virulence | abricate_virulence toolshed.g2.bx.psu.edu/repos/iuc/abricate/abricate/1.0.1 |
| 7 | ToolDistillator | ToolDistillator extracts results from tools and creates a JSON file for each tool toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator/tooldistillator/0.9.1+galaxy0 |
| 8 | ToolDistillator summarize | ToolDistillator summarize groups all JSON file into a unique JSON file toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator_summarize/tooldistillator_summarize/0.9.1+galaxy0 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| abricate_virulence_report | #main/abricate_virulence_report | n/a |
|
| amrfinderplus_mutation | #main/amrfinderplus_mutation | n/a |
|
| amrfinderplus_nucleotide | #main/amrfinderplus_nucleotide | n/a |
|
| amrfinderplus_report | #main/amrfinderplus_report | n/a |
|
| staramr_blast_hits | #main/staramr_blast_hits | n/a |
|
| staramr_detailed_summary | #main/staramr_detailed_summary | n/a |
|
| staramr_excel_report | #main/staramr_excel_report | n/a |
|
| staramr_mlst_report | #main/staramr_mlst_report | n/a |
|
| staramr_plasmidfinder_report | #main/staramr_plasmidfinder_report | n/a |
|
| staramr_resfinder_report | #main/staramr_resfinder_report | n/a |
|
| staramr_settings | #main/staramr_settings | n/a |
|
| staramr_summary | #main/staramr_summary | n/a |
|
| tooldistillator_results | #main/tooldistillator_results | n/a |
|
| tooldistillator_summarize | #main/tooldistillator_summarize | n/a |
|
Version History
v1.1.7 (latest) Created 4th Dec 2025 at 03:02 by WorkflowHub Bot
Updated to v1.1.7
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v1.1.73c9f016
v1.0 (earliest) Created 19th Jun 2024 at 03:01 by WorkflowHub Bot
Updated to v1.0
Frozen
v1.0
68bff5a
Creators and Submitter
Activity
Views: 9312 Downloads: 33809 Runs: 5
Created: 19th Jun 2024 at 03:01
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