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

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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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-1:000000000000 0:cbbe42422d56
1 pipeline:
2
3 # Download example data
4 - reader.URLReader:
5 url: https://gitlab01.classe.cornell.edu/api/v4/projects/308/repository/files/edd%2fdata.tar/raw?ref=main
6 headers:
7 PRIVATE-TOKEN: # your token here
8 - processor.URLResponseProcessor
9 - writer.ExtractArchiveWriter:
10 filename: examples/edd
11
12 # Calibrate detector
13 - reader.YAMLReader:
14 filename: examples/edd/ceria_calibration_config.yaml
15 schema: MCACeriaCalibrationConfig
16 - processor.MCACeriaCalibrationProcessor
17 - writer.YAMLWriter:
18 filename: examples/edd/ceria_calibrated.yaml
19 force_overwrite: true
20
21 # Gather calibrated detector data
22 - reader.MultipleReader:
23 readers:
24 - YAMLReader:
25 filename: examples/edd/map.yaml
26 schema: MapConfig
27 - YAMLReader:
28 filename: examples/edd/ceria_calibrated.yaml
29 schema: MCACeriaCalibrationConfig
30 - processor.MCADataProcessor
31 - writer.NexusWriter:
32 filename: examples/edd/map_detector_data.nxs
33 force_overwrite: true
34
35 # Compute sample strain map
36 - reader.MultipleReader:
37 readers:
38 - NexusReader:
39 filename: examples/edd/map_detector_data.nxs
40 - YAMLReader:
41 filename: examples/edd/strain_analysis_config.yaml
42 schema: StrainAnalysisConfig
43 - processor.StrainAnalysisProcessor
44 - writer.YAMLWriter:
45 filename: examples/edd/map_strain_data.yaml
46 force_overwrite: true
47