diff 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
parents
children
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/examples/edd/pipeline.yaml	Tue Mar 28 15:07:30 2023 +0000
@@ -0,0 +1,47 @@
+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
+