The Galaxy agentic stack

class: GalaxyUserTool
id: gff-seqname-map
version: "0.1.0"
name: Rename GFF sequence names
description: Rewrite column 1 of a GFF3 file from a two-column mapping; fail on unknown names
container: python:3.11-slim
shell_command: |
  python - '$(inputs.gff.path)' '$(inputs.mapping.path)' renamed.gff3 <<'PY'
  import sys
  gff, mapfile, out = sys.argv[1:4]
  names = {}
  with open(mapfile) as fh:
      for line in fh:
          if line.startswith('#') or not line.strip():
              continue
          old, new = line.rstrip('\n').split('\t')[:2]
          names[old] = new
  renamed = unknown = 0
  missing = set()
  with open(gff) as fin, open(out, 'w') as fout:
      for line in fin:
          if line.startswith('#') or not line.strip():
              fout.write(line)
              continue
          cols = line.split('\t')
          if cols[0] in names:
              cols[0] = names[cols[0]]
              renamed += 1
          else:
              unknown += 1
              missing.add(cols[0])
          fout.write('\t'.join(cols))
  print(f'renamed {renamed} feature lines; {len(names)} names mapped; {unknown} unknown')
  if unknown:
      print('unknown sequence names: ' + ', '.join(sorted(missing)), file=sys.stderr)
      sys.exit(2)
  PY
inputs:
  - name: gff
    type: data
    format: gff3
    label: GFF3 annotation
  - name: mapping
    type: data
    format: tabular
    label: Two-column mapping (old name, new name)
outputs:
  - name: renamed
    type: data
    format: gff3
    from_work_dir: renamed.gff3
help:
  format: markdown
  content: |
    Rewrites the sequence name (column 1) of every feature line in a GFF3 file
    using a two-column tab-separated mapping of old name to new name. Comment
    and blank lines pass through unchanged. The job fails if a sequence name is
    missing from the mapping; stdout reports how many lines changed.