amr_gene_detection/main

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Workflow Type: Galaxy

Antimicrobial resistance gene detection from assembled bacterial genomes

SEEK ID: https://workflowhub.eu/workflows/1049?version=2

Inputs

ID Name Description Type
Input sequence fasta #main/Input sequence fasta Can be any fasta file.
  • File
Select a AMR genes detection database #main/Select a AMR genes detection database Select the database to identify AMR genes with AMRFinderPlus.
  • string
Select a taxonomy group point mutation #main/Select a taxonomy group point mutation Select the database to identify resistance-associated point mutations with AMRFinderPlus.
  • string
Select a virulence genes detection database #main/Select a virulence genes detection database Select the database to identify virulence genes with ABRicate..
  • string

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/0.8.5.0+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/0.8.5.0+galaxy0

Outputs

ID Name Description Type
abricate_virulence_report #main/abricate_virulence_report n/a
  • File
amrfinderplus_mutation #main/amrfinderplus_mutation n/a
  • File
amrfinderplus_nucleotide #main/amrfinderplus_nucleotide n/a
  • File
amrfinderplus_report #main/amrfinderplus_report n/a
  • File
staramr_blast_hits #main/staramr_blast_hits n/a
  • File
staramr_detailed_summary #main/staramr_detailed_summary n/a
  • File
staramr_excel_report #main/staramr_excel_report n/a
  • File
staramr_mlst_report #main/staramr_mlst_report n/a
  • File
staramr_plasmidfinder_report #main/staramr_plasmidfinder_report n/a
  • File
staramr_resfinder_report #main/staramr_resfinder_report n/a
  • File
staramr_settings #main/staramr_settings n/a
  • File
staramr_summary #main/staramr_summary n/a
  • File
tooldistillator_results #main/tooldistillator_results n/a
  • File
tooldistillator_summarize #main/tooldistillator_summarize n/a
  • File

Version History

v1.1.1 (latest) Created 11th Jul 2024 at 03:02 by WorkflowHub Bot

Updated to v1.1.1


Frozen v1.1.1 25aa875

v1.1 Created 25th Jun 2024 at 03:02 by WorkflowHub Bot

Updated to v1.1


Frozen v1.1 677c843

v1.0 (earliest) Created 19th Jun 2024 at 03:01 by WorkflowHub Bot

Updated to v1.0


Frozen v1.0 68bff5a
help Creators and Submitter
Creators
  • ABRomics
  • Pierre Marin
  • Clea Siguret
Additional credit

abromics-consortium

Submitter
License
GNU General Public License v3.0 or later
Activity

Views: 993   Downloads: 222   Runs: 0

Created: 19th Jun 2024 at 03:01

help Attributions

None

Total size: 38.7 KB
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