# Tool-install request for use case: differential ATAC-seq accessibility
# Issue:    https://github.com/jmchilton/galaxy-brain/issues/14
# GTN anchors (repo names verbatim from their workflow .ga files):
#   - epigenetics/atac-seq  (iuc/macs2, iuc/bedtools, iuc/pygenometracks,
#                            bgruening/deeptools_compute_matrix, bgruening/deeptools_plot_heatmap)
#   - differential tools confirmed from other GTN workflows:
#                            iuc/featurecounts, iuc/deseq2, iuc/volcanoplot
# Deviation: single-sample peak calling -> replicate-aware counts over a shared peak
#            universe + DESeq2 differential testing. Single-sample preprocessing
#            (trimming/mapping/filtering/dup-removal) is intentionally omitted; MVP starts
#            from a prepared count matrix / union peaks.
tools:
# Peak calling (reused) + union peak-universe construction (merge/sort intervals)
- name: macs2
  owner: iuc
  tool_panel_section_label: 'Differential ATAC-seq'
- name: bedtools
  owner: iuc
  tool_panel_section_label: 'Differential ATAC-seq'
# Build SAF-like annotation from union peaks; filter significant DESeq2 hits
- name: text_processing
  owner: bgruening
  tool_panel_section_label: 'Differential ATAC-seq'
# Count fragments over the union peak universe
- name: featurecounts
  owner: iuc
  tool_panel_section_label: 'Differential ATAC-seq'
# Differential accessibility testing (factor: condition); PCA + sample-distance outputs
- name: deseq2
  owner: iuc
  tool_panel_section_label: 'Differential ATAC-seq'
# Volcano plot of differential accessibility
- name: volcanoplot
  owner: iuc
  tool_panel_section_label: 'Differential ATAC-seq'
# Replicate QC when BAMs are included
- name: deeptools_multi_bam_summary
  owner: bgruening
  tool_panel_section_label: 'Differential ATAC-seq'
- name: deeptools_plot_correlation
  owner: bgruening
  tool_panel_section_label: 'Differential ATAC-seq'
# Signal heatmap/profile over top differential peaks
- name: deeptools_compute_matrix
  owner: bgruening
  tool_panel_section_label: 'Differential ATAC-seq'
- name: deeptools_plot_heatmap
  owner: bgruening
  tool_panel_section_label: 'Differential ATAC-seq'
# Genome-track figure over a gained/lost region
- name: pygenometracks
  owner: iuc
  tool_panel_section_label: 'Differential ATAC-seq'