# Tool-install request for use case: MRSA mobile-AMR context across isolates
# Issue:    https://github.com/jmchilton/galaxy-brain/issues/12
# GTN anchors (repo names taken verbatim from their workflow .ga files):
#   - genome-annotation/amr-gene-detection      (nml/staramr, iuc/bakta, iuc/tbl2gff3, iuc/jbrowse)
#   - genome-annotation/bacterial-genome-annotation
#                                               (iuc/isescan, iuc/integron_finder, iuc/plasmidfinder,
#                                                bgruening/text_processing)
# Deviation: comparative ARG mobile-context across 3-4 isolates. Read QC/assembly is
#            provenance only and intentionally omitted; heatmaps/figures are rendered in-notebook.
tools:
# AMR detection over the isolate-assembly collection (summary/resfinder/plasmidfinder/mlst TSVs)
- name: staramr
  owner: nml
  tool_panel_section_label: 'MRSA Mobile AMR'
# Whole-genome annotation per isolate
- name: bakta
  owner: iuc
  tool_panel_section_label: 'MRSA Mobile AMR'
# Mobile genetic element calls: insertion sequences and integrons
- name: isescan
  owner: iuc
  tool_panel_section_label: 'MRSA Mobile AMR'
- name: integron_finder
  owner: iuc
  tool_panel_section_label: 'MRSA Mobile AMR'
# Plasmid replicon typing (standalone, for coordinates feeding the mobile-context map)
- name: plasmidfinder
  owner: iuc
  tool_panel_section_label: 'MRSA Mobile AMR'
# Convert AMR/plasmid/IS/integron tables into GFF3 intervals
- name: tbl2gff3
  owner: iuc
  tool_panel_section_label: 'MRSA Mobile AMR'
# General table wrangling for the same conversions (cut/sort/awk/sed)
- name: text_processing
  owner: bgruening
  tool_panel_section_label: 'MRSA Mobile AMR'
# Interval intersect/closest to classify ARGs as plasmid/IS/integron-adjacent
- name: bedtools
  owner: iuc
  tool_panel_section_label: 'MRSA Mobile AMR'
# Locus visualization for the representative mobile-AMR region
- name: jbrowse
  owner: iuc
  tool_panel_section_label: 'MRSA Mobile AMR'