feat: add clt conversion

PolusAI · Mar 19, 2024 · 3fa5a57 · 3fa5a57
1 parent 9f45607
commit 3fa5a57
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diff --git a/clustering/K-NN/Shared-Memory-GPU/k-nn(cuda).cwl b/clustering/K-NN/Shared-Memory-GPU/k-nn(cuda).cwl
@@ -0,0 +1,28 @@
+class: CommandLineTool
+cwlVersion: v1.2
+inputs:
+  K:
+    inputBinding:
+      prefix: --K
+    type: double
+  convThreshold:
+    inputBinding:
+      prefix: --convThreshold
+    type: double
+  inputPath:
+    inputBinding:
+      prefix: --inputPath
+    type: Directory
+  outputPath:
+    inputBinding:
+      prefix: --outputPath
+    type: Directory
+  sampleRate:
+    inputBinding:
+      prefix: --sampleRate
+    type: double
+outputs:
+  outputPath: !!python/name:builtins.NotImplementedError ''
+requirements:
+  DockerRequirement:
+    dockerPull: labshare/polus-knn-plugin:cuda-0.1.0
diff --git a/clustering/K-NN/Shared-Memory-Serial/k-nn(serial).cwl b/clustering/K-NN/Shared-Memory-Serial/k-nn(serial).cwl
@@ -0,0 +1,28 @@
+class: CommandLineTool
+cwlVersion: v1.2
+inputs:
+  K:
+    inputBinding:
+      prefix: --K
+    type: double
+  convThreshold:
+    inputBinding:
+      prefix: --convThreshold
+    type: double
+  inputPath:
+    inputBinding:
+      prefix: --inputPath
+    type: Directory
+  outputPath:
+    inputBinding:
+      prefix: --outputPath
+    type: Directory
+  sampleRate:
+    inputBinding:
+      prefix: --sampleRate
+    type: double
+outputs:
+  outputPath: !!python/name:builtins.NotImplementedError ''
+requirements:
+  DockerRequirement:
+    dockerPull: labshare/polus-knn-plugin:serial-0.1.0
diff --git a/clustering/k-means-clustering-tool/k-meansclustering.cwl b/clustering/k-means-clustering-tool/k-meansclustering.cwl
@@ -0,0 +1,48 @@
+class: CommandLineTool
+cwlVersion: v1.2
+inputs:
+  filePattern:
+    inputBinding:
+      prefix: --filePattern
+    type: string?
+  inpDir:
+    inputBinding:
+      prefix: --inpDir
+    type: Directory
+  maximumRange:
+    inputBinding:
+      prefix: --maximumRange
+    type: double?
+  methods:
+    inputBinding:
+      prefix: --methods
+    type: string
+  minimumRange:
+    inputBinding:
+      prefix: --minimumRange
+    type: double?
+  numOfClus:
+    inputBinding:
+      prefix: --numOfClus
+    type: double?
+  outDir:
+    inputBinding:
+      prefix: --outDir
+    type: Directory
+  preview:
+    inputBinding:
+      prefix: --preview
+    type: boolean?
+outputs:
+  outDir:
+    outputBinding:
+      glob: $(inputs.outDir.basename)
+    type: Directory
+requirements:
+  DockerRequirement:
+    dockerPull: polusai/k-means-clustering-tool:0.3.5-dev0
+  InitialWorkDirRequirement:
+    listing:
+    - entry: $(inputs.outDir)
+      writable: true
+  InlineJavascriptRequirement: {}
diff --git a/clustering/outlier-removal-tool/outlierremoval.cwl b/clustering/outlier-removal-tool/outlierremoval.cwl
@@ -0,0 +1,40 @@
+class: CommandLineTool
+cwlVersion: v1.2
+inputs:
+  filePattern:
+    inputBinding:
+      prefix: --filePattern
+    type: string?
+  inpDir:
+    inputBinding:
+      prefix: --inpDir
+    type: Directory
+  method:
+    inputBinding:
+      prefix: --method
+    type: string?
+  outDir:
+    inputBinding:
+      prefix: --outDir
+    type: Directory
+  outputType:
+    inputBinding:
+      prefix: --outputType
+    type: string?
+  preview:
+    inputBinding:
+      prefix: --preview
+    type: boolean?
+outputs:
+  outDir:
+    outputBinding:
+      glob: $(inputs.outDir.basename)
+    type: Directory
+requirements:
+  DockerRequirement:
+    dockerPull: polusai/outlier-removal-tool:0.2.7-dev0
+  InitialWorkDirRequirement:
+    listing:
+    - entry: $(inputs.outDir)
+      writable: true
+  InlineJavascriptRequirement: {}
diff --git a/clustering/polus-feature-subsetting-plugin/featuresubsetting.cwl b/clustering/polus-feature-subsetting-plugin/featuresubsetting.cwl
@@ -0,0 +1,60 @@
+class: CommandLineTool
+cwlVersion: v1.2
+inputs:
+  csvDir:
+    inputBinding:
+      prefix: --csvDir
+    type: Directory
+  feature:
+    inputBinding:
+      prefix: --feature
+    type: string
+  filePattern:
+    inputBinding:
+      prefix: --filePattern
+    type: string
+  groupVar:
+    inputBinding:
+      prefix: --groupVar
+    type: string
+  inpDir:
+    inputBinding:
+      prefix: --inpDir
+    type: Directory
+  outDir:
+    inputBinding:
+      prefix: --outDir
+    type: Directory
+  padding:
+    inputBinding:
+      prefix: --padding
+    type: string?
+  percentile:
+    inputBinding:
+      prefix: --percentile
+    type: double
+  removeDirection:
+    inputBinding:
+      prefix: --removeDirection
+    type: string
+  sectionVar:
+    inputBinding:
+      prefix: --sectionVar
+    type: string?
+  writeOutput:
+    inputBinding:
+      prefix: --writeOutput
+    type: boolean?
+outputs:
+  outDir:
+    outputBinding:
+      glob: $(inputs.outDir.basename)
+    type: Directory
+requirements:
+  DockerRequirement:
+    dockerPull: polusai/feature-subsetting-plugin:0.1.11
+  InitialWorkDirRequirement:
+    listing:
+    - entry: $(inputs.outDir)
+      writable: true
+  InlineJavascriptRequirement: {}
diff --git a/clustering/polus-hdbscan-clustering-plugin/hdbscanclustering.cwl b/clustering/polus-hdbscan-clustering-plugin/hdbscanclustering.cwl
@@ -0,0 +1,44 @@
+class: CommandLineTool
+cwlVersion: v1.2
+inputs:
+  averageGroups:
+    inputBinding:
+      prefix: --averageGroups
+    type: boolean?
+  groupingPattern:
+    inputBinding:
+      prefix: --groupingPattern
+    type: string?
+  incrementOutlierId:
+    inputBinding:
+      prefix: --incrementOutlierId
+    type: boolean?
+  inpDir:
+    inputBinding:
+      prefix: --inpDir
+    type: Directory
+  labelCol:
+    inputBinding:
+      prefix: --labelCol
+    type: string?
+  minClusterSize:
+    inputBinding:
+      prefix: --minClusterSize
+    type: double
+  outDir:
+    inputBinding:
+      prefix: --outDir
+    type: Directory
+outputs:
+  outDir:
+    outputBinding:
+      glob: $(inputs.outDir.basename)
+    type: Directory
+requirements:
+  DockerRequirement:
+    dockerPull: polusai/hdbscan-clustering-plugin:0.4.7
+  InitialWorkDirRequirement:
+    listing:
+    - entry: $(inputs.outDir)
+      writable: true
+  InlineJavascriptRequirement: {}
diff --git a/dimension_reduction/UMAP/Shared-Memory-GPU/umap(cuda).cwl b/dimension_reduction/UMAP/Shared-Memory-GPU/umap(cuda).cwl
@@ -0,0 +1,56 @@
+class: CommandLineTool
+cwlVersion: v1.2
+inputs:
+  DimLowSpace:
+    inputBinding:
+      prefix: --DimLowSpace
+    type: double
+  K:
+    inputBinding:
+      prefix: --K
+    type: double
+  distanceMetric:
+    inputBinding:
+      prefix: --distanceMetric
+    type: string
+  distanceV1:
+    inputBinding:
+      prefix: --distanceV1
+    type: double?
+  distanceV2:
+    inputBinding:
+      prefix: --distanceV2
+    type: double?
+  inputPath:
+    inputBinding:
+      prefix: --inputPath
+    type: Directory
+  inputPathOptionalArray:
+    inputBinding:
+      prefix: --inputPathOptionalArray
+    type: Directory?
+  minDist:
+    inputBinding:
+      prefix: --minDist
+    type: double
+  nEpochs:
+    inputBinding:
+      prefix: --nEpochs
+    type: double
+  outputPath:
+    inputBinding:
+      prefix: --outputPath
+    type: Directory
+  randomInitializing:
+    inputBinding:
+      prefix: --randomInitializing
+    type: boolean
+  sampleRate:
+    inputBinding:
+      prefix: --sampleRate
+    type: double
+outputs:
+  outputPath: !!python/name:builtins.NotImplementedError ''
+requirements:
+  DockerRequirement:
+    dockerPull: labshare/polus-umap-cuda-plugin:0.1.0
diff --git a/features/feature-segmentation-eval-tool/featuresegmentationeval.cwl b/features/feature-segmentation-eval-tool/featuresegmentationeval.cwl
@@ -0,0 +1,44 @@
+class: CommandLineTool
+cwlVersion: v1.2
+inputs:
+  GTDir:
+    inputBinding:
+      prefix: --GTDir
+    type: Directory
+  PredDir:
+    inputBinding:
+      prefix: --PredDir
+    type: Directory
+  combineLabels:
+    inputBinding:
+      prefix: --combineLabels
+    type: boolean?
+  filePattern:
+    inputBinding:
+      prefix: --filePattern
+    type: string?
+  outDir:
+    inputBinding:
+      prefix: --outDir
+    type: Directory
+  preview:
+    inputBinding:
+      prefix: --preview
+    type: boolean?
+  singleOutFile:
+    inputBinding:
+      prefix: --singleOutFile
+    type: boolean?
+outputs:
+  outDir:
+    outputBinding:
+      glob: $(inputs.outDir.basename)
+    type: Directory
+requirements:
+  DockerRequirement:
+    dockerPull: polusai/feature-segmentation-eval-tool:0.2.6-dev0
+  InitialWorkDirRequirement:
+    listing:
+    - entry: $(inputs.outDir)
+      writable: true
+  InlineJavascriptRequirement: {}