# Tool-install request for use case: TAL1 peaks to candidate regulated genes
# Issue:    https://github.com/jmchilton/galaxy-brain/issues/13
# GTN anchors (repo names verbatim from their workflow .ga files):
#   - epigenetics/tal1-binding-site-identification (iuc/macs2, iuc/bedtools, bgruening/deeptools_*)
#   - transcriptomics/de-novo                      (stretch: expression evidence join)
# Deviation: reuse the tutorial's existing narrowPeak / peak-class outputs and close the
#            interpretive loop -> promoter-overlap + nearest-gene candidate prioritization.
#            Trackster/IGV-style browsing is a built-in Galaxy view (no install). Bar charts /
#            distance-to-TSS distributions are rendered in-notebook.
tools:
# Promoter-window construction (slop/flank), peak<->promoter Intersect, nearest-gene ClosestBed
- name: bedtools
  owner: iuc
  tool_panel_section_label: 'TAL1 Candidate Genes'
# Collapse duplicate transcript isoforms by gene symbol; stretch expression-table join
- name: text_processing
  owner: bgruening
  tool_panel_section_label: 'TAL1 Candidate Genes'
# Provenance: the reused TAL1 peaks were called with MACS2 in the source tutorial.
# Included so the notebook can regenerate peaks if upstream outputs are unavailable.
- name: macs2
  owner: iuc
  tool_panel_section_label: 'TAL1 Candidate Genes'