view examples/edd/pipeline.yaml @ 0:cbbe42422d56 draft

planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
author kls286
date Tue, 28 Mar 2023 15:07:30 +0000
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pipeline:

  # Download example data
  - reader.URLReader:
      url: https://gitlab01.classe.cornell.edu/api/v4/projects/308/repository/files/edd%2fdata.tar/raw?ref=main
      headers:
        PRIVATE-TOKEN: # your token here
  - processor.URLResponseProcessor
  - writer.ExtractArchiveWriter:
      filename: examples/edd

  # Calibrate detector
  - reader.YAMLReader:
      filename: examples/edd/ceria_calibration_config.yaml
      schema: MCACeriaCalibrationConfig
  - processor.MCACeriaCalibrationProcessor
  - writer.YAMLWriter:
      filename: examples/edd/ceria_calibrated.yaml
      force_overwrite: true

  # Gather calibrated detector data
  - reader.MultipleReader:
      readers:
        - YAMLReader:
            filename: examples/edd/map.yaml
            schema: MapConfig
        - YAMLReader:
            filename: examples/edd/ceria_calibrated.yaml
            schema: MCACeriaCalibrationConfig
  - processor.MCADataProcessor
  - writer.NexusWriter:
      filename: examples/edd/map_detector_data.nxs
      force_overwrite: true

  # Compute sample strain map
  - reader.MultipleReader:
      readers:
        - NexusReader:
            filename: examples/edd/map_detector_data.nxs
        - YAMLReader:
            filename: examples/edd/strain_analysis_config.yaml
            schema: StrainAnalysisConfig
  - processor.StrainAnalysisProcessor
  - writer.YAMLWriter:
      filename: examples/edd/map_strain_data.yaml
      force_overwrite: true