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hamshkhawarhamshkhawar
committed
refactored code
1 parent 24f7f83 commit 0d7aa66

15 files changed

+445
-34
lines changed

‎cwl_adapters/BbbcDownload.cwl

+29
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class: CommandLineTool
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cwlVersion: v1.2
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inputs:
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name:
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inputBinding:
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prefix: --name
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type: string
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outDir:
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inputBinding:
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prefix: --outDir
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type: Directory
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outputs:
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outDir:
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outputBinding:
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glob: $(inputs.outDir.basename)
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type: Directory
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requirements:
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DockerRequirement:
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dockerPull: polusai/bbbc-download-plugin:0.1.0-dev1
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EnvVarRequirement:
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envDef:
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HOME: /home/polusai
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InitialWorkDirRequirement:
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listing:
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- entry: $(inputs.outDir)
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writable: true
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InlineJavascriptRequirement: {}
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NetworkAccess:
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networkAccess: true

‎cwl_adapters/FileRenaming.cwl

+41
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class: CommandLineTool
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cwlVersion: v1.2
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inputs:
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filePattern:
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inputBinding:
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prefix: --filePattern
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type: string
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inpDir:
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inputBinding:
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prefix: --inpDir
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type: Directory
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mapDirectory:
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inputBinding:
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prefix: --mapDirectory
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type: boolean?
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outDir:
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inputBinding:
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prefix: --outDir
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type: Directory
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outFilePattern:
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inputBinding:
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prefix: --outFilePattern
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type: string
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outputs:
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outDir:
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outputBinding:
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glob: $(inputs.outDir.basename)
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type: Directory
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requirements:
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DockerRequirement:
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dockerPull: polusai/file-renaming-tool:0.2.4-dev1
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EnvVarRequirement:
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envDef:
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HOME: /home/polusai
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InitialWorkDirRequirement:
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listing:
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- entry: $(inputs.outDir)
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writable: true
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InlineJavascriptRequirement: {}
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NetworkAccess:
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networkAccess: true

‎cwl_adapters/FtlLabel.cwl

+37
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class: CommandLineTool
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cwlVersion: v1.2
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inputs:
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binarizationThreshold:
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inputBinding:
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prefix: --binarizationThreshold
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type: double
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connectivity:
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inputBinding:
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prefix: --connectivity
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type: string
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inpDir:
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inputBinding:
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prefix: --inpDir
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type: Directory
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outDir:
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inputBinding:
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prefix: --outDir
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type: Directory
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outputs:
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outDir:
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outputBinding:
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glob: $(inputs.outDir.basename)
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type: Directory
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requirements:
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DockerRequirement:
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dockerPull: polusai/ftl-label-plugin:0.3.12-dev5
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EnvVarRequirement:
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envDef:
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HOME: /home/polusai
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InitialWorkDirRequirement:
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listing:
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- entry: $(inputs.outDir)
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writable: true
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InlineJavascriptRequirement: {}
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NetworkAccess:
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networkAccess: true

‎cwl_adapters/ImageAssembler.cwl

+41
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@@ -0,0 +1,41 @@
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class: CommandLineTool
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cwlVersion: v1.2
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inputs:
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imgPath:
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inputBinding:
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prefix: --imgPath
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type: Directory
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outDir:
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inputBinding:
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prefix: --outDir
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type: Directory
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preview:
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inputBinding:
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prefix: --preview
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type: boolean?
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stitchPath:
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inputBinding:
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prefix: --stitchPath
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type: Directory
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timesliceNaming:
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inputBinding:
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prefix: --timesliceNaming
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type: boolean?
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outputs:
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outDir:
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outputBinding:
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glob: $(inputs.outDir.basename)
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type: Directory
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requirements:
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DockerRequirement:
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dockerPull: polusai/image-assembler-tool:1.4.2
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EnvVarRequirement:
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envDef:
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HOME: /home/polusai
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InitialWorkDirRequirement:
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listing:
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- entry: $(inputs.outDir)
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writable: true
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InlineJavascriptRequirement: {}
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NetworkAccess:
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networkAccess: true

‎cwl_adapters/KaggleNucleiSegmentation.cwl

+37
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class: CommandLineTool
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cwlVersion: v1.2
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inputs:
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filePattern:
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inputBinding:
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prefix: --filePattern
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type: string?
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inpDir:
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inputBinding:
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prefix: --inpDir
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type: Directory
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outDir:
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inputBinding:
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prefix: --outDir
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type: Directory
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preview:
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inputBinding:
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prefix: --preview
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type: boolean?
20+
outputs:
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outDir:
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outputBinding:
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glob: $(inputs.outDir.basename)
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type: Directory
25+
requirements:
26+
DockerRequirement:
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dockerPull: polusai/kaggle-nuclei-segmentation-tool:0.1.5-dev1
28+
EnvVarRequirement:
29+
envDef:
30+
HOME: /home/polusai
31+
InitialWorkDirRequirement:
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listing:
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- entry: $(inputs.outDir)
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writable: true
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InlineJavascriptRequirement: {}
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NetworkAccess:
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networkAccess: true

‎cwl_adapters/Montage.cwl

+49
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class: CommandLineTool
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cwlVersion: v1.2
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inputs:
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filePattern:
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inputBinding:
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prefix: --filePattern
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type: string
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flipAxis:
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inputBinding:
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prefix: --flipAxis
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type: string?
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gridSpacing:
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inputBinding:
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prefix: --gridSpacing
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type: string?
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imageSpacing:
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inputBinding:
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prefix: --imageSpacing
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type: string?
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inpDir:
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inputBinding:
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prefix: --inpDir
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type: Directory
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layout:
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inputBinding:
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prefix: --layout
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type: string?
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outDir:
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inputBinding:
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prefix: --outDir
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type: Directory
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outputs:
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outDir:
34+
outputBinding:
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glob: $(inputs.outDir.basename)
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type: Directory
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requirements:
38+
DockerRequirement:
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dockerPull: polusai/montage-tool:0.5.1
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EnvVarRequirement:
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envDef:
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HOME: /home/polusai
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InitialWorkDirRequirement:
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listing:
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- entry: $(inputs.outDir)
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writable: true
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InlineJavascriptRequirement: {}
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NetworkAccess:
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networkAccess: true

‎cwl_adapters/NyxusPlugin.cwl

+61
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@@ -0,0 +1,61 @@
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class: CommandLineTool
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cwlVersion: v1.2
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inputs:
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features:
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inputBinding:
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prefix: --features
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type: string?
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fileExtension:
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inputBinding:
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prefix: --fileExtension
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type: string
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inpDir:
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inputBinding:
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prefix: --inpDir
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type: Directory
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intPattern:
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inputBinding:
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prefix: --intPattern
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type: string
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neighborDist:
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inputBinding:
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prefix: --neighborDist
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type: double?
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outDir:
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inputBinding:
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prefix: --outDir
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type: Directory
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pixelPerMicron:
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inputBinding:
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prefix: --pixelPerMicron
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type: double?
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segDir:
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inputBinding:
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prefix: --segDir
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type: Directory
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segPattern:
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inputBinding:
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prefix: --segPattern
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type: string
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singleRoi:
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inputBinding:
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prefix: --singleRoi
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type: boolean?
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outputs:
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outDir:
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outputBinding:
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glob: $(inputs.outDir.basename)
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type: Directory
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requirements:
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DockerRequirement:
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dockerPull: polusai/nyxus-tool:0.1.8
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EnvVarRequirement:
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envDef:
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HOME: /home/polusai
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InitialWorkDirRequirement:
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listing:
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- entry: $(inputs.outDir)
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writable: true
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InlineJavascriptRequirement: {}
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NetworkAccess:
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networkAccess: true

‎cwl_adapters/OmeConverter.cwl

+37
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@@ -0,0 +1,37 @@
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class: CommandLineTool
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cwlVersion: v1.2
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inputs:
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fileExtension:
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inputBinding:
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prefix: --fileExtension
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type: string
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filePattern:
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inputBinding:
10+
prefix: --filePattern
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type: string
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inpDir:
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inputBinding:
14+
prefix: --inpDir
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type: Directory
16+
outDir:
17+
inputBinding:
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prefix: --outDir
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type: Directory
20+
outputs:
21+
outDir:
22+
outputBinding:
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glob: $(inputs.outDir.basename)
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type: Directory
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requirements:
26+
DockerRequirement:
27+
dockerPull: polusai/ome-converter-plugin:0.3.2-dev2
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EnvVarRequirement:
29+
envDef:
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HOME: /home/polusai
31+
InitialWorkDirRequirement:
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listing:
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- entry: $(inputs.outDir)
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writable: true
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InlineJavascriptRequirement: {}
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NetworkAccess:
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networkAccess: true

‎cwl_adapters/PrecomputeSlide.cwl

+41
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@@ -0,0 +1,41 @@
1+
class: CommandLineTool
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cwlVersion: v1.2
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inputs:
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filePattern:
5+
inputBinding:
6+
prefix: --filePattern
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type: string?
8+
imageType:
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inputBinding:
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prefix: --imageType
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type: string?
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inpDir:
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inputBinding:
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prefix: --inpDir
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type: Directory
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outDir:
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inputBinding:
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prefix: --outDir
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type: Directory
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pyramidType:
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inputBinding:
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prefix: --pyramidType
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type: string
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outputs:
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outDir:
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outputBinding:
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glob: $(inputs.outDir.basename)
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type: Directory
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requirements:
30+
DockerRequirement:
31+
dockerPull: polusai/precompute-slide-tool:1.7.2
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EnvVarRequirement:
33+
envDef:
34+
HOME: /home/polusai
35+
InitialWorkDirRequirement:
36+
listing:
37+
- entry: $(inputs.outDir)
38+
writable: true
39+
InlineJavascriptRequirement: {}
40+
NetworkAccess:
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networkAccess: true

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