Mercurial > repos > kls286 > chap_test_20230328

annotate saxswaxs-config/pipeline.yaml @ 15:c01900e93daa draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 52e0f071d66addeaabb3b5ad28bb4734b6f7cece-dirty
author kls286
date Thu, 30 Mar 2023 14:38:19 +0000
parents
children f7133218d7c3
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
15
c01900e93daa planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 52e0f071d66addeaabb3b5ad28bb4734b6f7cece-dirty
kls286
parents:
diff changeset
1 pipeline:
c01900e93daa planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 52e0f071d66addeaabb3b5ad28bb4734b6f7cece-dirty
kls286
parents:
diff changeset
2
c01900e93daa planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 52e0f071d66addeaabb3b5ad28bb4734b6f7cece-dirty
kls286
parents:
diff changeset
3 # Download example data
c01900e93daa planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 52e0f071d66addeaabb3b5ad28bb4734b6f7cece-dirty
kls286
parents:
diff changeset
4 - reader.URLReader:
c01900e93daa planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 52e0f071d66addeaabb3b5ad28bb4734b6f7cece-dirty
kls286
parents:
diff changeset
5 url: https://gitlab01.classe.cornell.edu/api/v4/projects/308/repository/files/saxswaxs%2frawdata_test_1d.tar/raw?ref=main
c01900e93daa planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 52e0f071d66addeaabb3b5ad28bb4734b6f7cece-dirty
kls286
parents:
diff changeset
6 headers:
c01900e93daa planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 52e0f071d66addeaabb3b5ad28bb4734b6f7cece-dirty
kls286
parents:
diff changeset
7 PRIVATE-TOKEN: glpat-sH-sniHbynCxUDJBpv5V # your token here
c01900e93daa planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 52e0f071d66addeaabb3b5ad28bb4734b6f7cece-dirty
kls286
parents:
diff changeset
8 - processor.URLResponseProcessor
c01900e93daa planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 52e0f071d66addeaabb3b5ad28bb4734b6f7cece-dirty
kls286
parents:
diff changeset
9 - writer.ExtractArchiveWriter:
c01900e93daa planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 52e0f071d66addeaabb3b5ad28bb4734b6f7cece-dirty
kls286
parents:
diff changeset
10 filename: .
c01900e93daa planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 52e0f071d66addeaabb3b5ad28bb4734b6f7cece-dirty
kls286
parents:
diff changeset
11
c01900e93daa planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 52e0f071d66addeaabb3b5ad28bb4734b6f7cece-dirty
kls286
parents:
diff changeset
12 # Collect map data
c01900e93daa planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 52e0f071d66addeaabb3b5ad28bb4734b6f7cece-dirty
kls286
parents:
diff changeset
13 - reader.YAMLReader:
c01900e93daa planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 52e0f071d66addeaabb3b5ad28bb4734b6f7cece-dirty
kls286
parents:
diff changeset
14 filename: map.yaml
c01900e93daa planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 52e0f071d66addeaabb3b5ad28bb4734b6f7cece-dirty
kls286
parents:
diff changeset
15 schema: MapConfig
c01900e93daa planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 52e0f071d66addeaabb3b5ad28bb4734b6f7cece-dirty
kls286
parents:
diff changeset
16 - processor.MapProcessor
c01900e93daa planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 52e0f071d66addeaabb3b5ad28bb4734b6f7cece-dirty
kls286
parents:
diff changeset
17 - writer.NexusWriter:
c01900e93daa planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 52e0f071d66addeaabb3b5ad28bb4734b6f7cece-dirty
kls286
parents:
diff changeset
18 filename: map_specdata.nxs
c01900e93daa planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 52e0f071d66addeaabb3b5ad28bb4734b6f7cece-dirty
kls286
parents:
diff changeset
19 force_overwrite: true
c01900e93daa planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 52e0f071d66addeaabb3b5ad28bb4734b6f7cece-dirty
kls286
parents:
diff changeset
20
c01900e93daa planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 52e0f071d66addeaabb3b5ad28bb4734b6f7cece-dirty
kls286
parents:
diff changeset
21 # Integrate map detetcor data
c01900e93daa planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 52e0f071d66addeaabb3b5ad28bb4734b6f7cece-dirty
kls286
parents:
diff changeset
22 - reader.MultipleReader:
c01900e93daa planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 52e0f071d66addeaabb3b5ad28bb4734b6f7cece-dirty
kls286
parents:
diff changeset
23 readers:
c01900e93daa planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 52e0f071d66addeaabb3b5ad28bb4734b6f7cece-dirty
kls286
parents:
diff changeset
24 - YAMLReader:
c01900e93daa planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 52e0f071d66addeaabb3b5ad28bb4734b6f7cece-dirty
kls286
parents:
diff changeset
25 filename: map.yaml
c01900e93daa planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 52e0f071d66addeaabb3b5ad28bb4734b6f7cece-dirty
kls286
parents:
diff changeset
26 schema: MapConfig
c01900e93daa planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 52e0f071d66addeaabb3b5ad28bb4734b6f7cece-dirty
kls286
parents:
diff changeset
27 - YAMLReader:
c01900e93daa planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 52e0f071d66addeaabb3b5ad28bb4734b6f7cece-dirty
kls286
parents:
diff changeset
28 filename: integration.yaml
c01900e93daa planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 52e0f071d66addeaabb3b5ad28bb4734b6f7cece-dirty
kls286
parents:
diff changeset
29 schema: IntegrationConfig
c01900e93daa planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 52e0f071d66addeaabb3b5ad28bb4734b6f7cece-dirty
kls286
parents:
diff changeset
30 - processor.IntegrateMapProcessor
c01900e93daa planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 52e0f071d66addeaabb3b5ad28bb4734b6f7cece-dirty
kls286
parents:
diff changeset
31 - writer.NexusWriter:
c01900e93daa planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 52e0f071d66addeaabb3b5ad28bb4734b6f7cece-dirty
kls286
parents:
diff changeset
32 filename: map_reduceddata.nxs
c01900e93daa planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 52e0f071d66addeaabb3b5ad28bb4734b6f7cece-dirty
kls286
parents:
diff changeset
33 force_overwrite: true