# HG changeset patch # User ximgchess # Date 1681389641 0 # Node ID 2679014bb6eb774c374e34bd45574bf863267dbb # Parent a560d5143348efe689f47b7ac7c10dd826de771b planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit e280dd942513f966a9a61a3af68ee7972fb8992f-dirty diff -r a560d5143348 -r 2679014bb6eb saxswaxs/ignoreshed.yml --- a/saxswaxs/ignoreshed.yml Thu Apr 13 12:18:11 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,7 +0,0 @@ -name: chap_test_20230328 -owner: kls286 -description: A generic test pipeline for CHAP -remote_repository_url: https://github.com/CHESSComputing/ChessAnalysisPipeline -type: unrestricted -categories: -- Structural Materials Analysis diff -r a560d5143348 -r 2679014bb6eb saxswaxs/klspipeline.yaml --- a/saxswaxs/klspipeline.yaml Thu Apr 13 12:18:11 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,33 +0,0 @@ -pipeline: - - # Download example data - - common.URLReader: - url: https://gitlab01.classe.cornell.edu/api/v4/projects/308/repository/files/saxswaxs%2frawdata_test_1d.tar/raw?ref=main - headers: - PRIVATE-TOKEN: glpat-sH-sniHbynCxUDJBpv5V # your token here - - common.URLResponseProcessor - - common.ExtractArchiveWriter: - filename: . - - # Collect map data - - common.YAMLReader: - filename: map.yaml - schema: MapConfig - - common.MapProcessor - - common.NexusWriter: - filename: map_specdata.nxs - force_overwrite: true - - # Integrate map detetcor data - - common.MultipleReader: - readers: - - YAMLReader: - filename: map.yaml - schema: MapConfig - - YAMLReader: - filename: integration.yaml - schema: IntegrationConfig - - common.IntegrateMapProcessor - - common.NexusWriter: - filename: map_reduceddata.nxs - force_overwrite: true diff -r a560d5143348 -r 2679014bb6eb tomo/pipeline_reduce_nexus.yaml --- a/tomo/pipeline_reduce_nexus.yaml Thu Apr 13 12:18:11 2023 +0000 +++ b/tomo/pipeline_reduce_nexus.yaml Thu Apr 13 12:40:41 2023 +0000 @@ -8,7 +8,9 @@ - YAMLReader: filename: reduce.yaml schema: TomoReduceConfig - - tomo.TomoDataProcessor + - tomo.TomoDataProcessor: + output_folder: tomo_reduce_plots + save_figs: 'only' - common.NexusWriter: filename: output.nex force_overwrite: true diff -r a560d5143348 -r 2679014bb6eb tomo/pipeline_reduce_yaml.yaml --- a/tomo/pipeline_reduce_yaml.yaml Thu Apr 13 12:18:11 2023 +0000 +++ b/tomo/pipeline_reduce_yaml.yaml Thu Apr 13 12:40:41 2023 +0000 @@ -9,7 +9,9 @@ - YAMLReader: filename: reduce.yaml schema: TomoReduceConfig - - tomo.TomoDataProcessor + - tomo.TomoDataProcessor: + output_folder: tomo_reduce_plots + save_figs: 'only' - common.NexusWriter: filename: output.nex force_overwrite: true diff -r a560d5143348 -r 2679014bb6eb tomo/tomo_macros.xml --- a/tomo/tomo_macros.xml Thu Apr 13 12:18:11 2023 +0000 +++ b/tomo/tomo_macros.xml Thu Apr 13 12:40:41 2023 +0000 @@ -1,10 +1,10 @@ 0.1.0 21.09 - 3.9.13 + 3.9 - chessanalysispipeline + chessanalysispipeline lmfit matplotlib nexusformat diff -r a560d5143348 -r 2679014bb6eb tomo/tomo_reduce.xml --- a/tomo/tomo_reduce.xml Thu Apr 13 12:18:11 2023 +0000 +++ b/tomo/tomo_reduce.xml Thu Apr 13 12:40:41 2023 +0000 @@ -7,32 +7,33 @@ reduce.yaml && #else - cp '$input_file' setup.nex && + cp $input_file setup.nex && + cp $tool_config reduce.yaml && #end if - cp '$tool_config' reduce.yaml && CHAP --config - #if str($map.type_selector) == "YAML" - '$__tool_directory__/pipeline_reduce_yaml.yaml' + #if str($map.type_selector) == "yaml" + $__tool_directory__/pipeline_reduce_yaml.yaml #else - '$__tool_directory__/pipeline_reduce_nexus.yaml' + $__tool_directory__/pipeline_reduce_nexus.yaml #end if ]]>