test(pythonapi): add initial tests for Python API

tests/resources/assembler.cwl

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+#!/usr/bin/env cwl-runner
+
+cwlVersion: v1.2
+class: CommandLineTool
+
+requirements:
+  DockerRequirement:
+    dockerPull: polusai/image-assembler-plugin:1.2.1-dev0
+  InitialWorkDirRequirement:
+    listing:
+    - writable: true
+      entry: $(inputs.outDir)
+  InlineJavascriptRequirement: {}
+
+inputs:
+  imgPath:
+    type: Directory
+    inputBinding:
+      prefix: --imgPath
+  outDir:
+    type: Directory
+    inputBinding:
+      prefix: --outDir
+  preview:
+    type: boolean?
+    inputBinding:
+      prefix: --preview
+  stitchPath:
+    type: Directory
+    inputBinding:
+      prefix: --stitchPath
+  timesliceNaming:
+    type: boolean?
+    inputBinding:
+      prefix: --timesliceNaming
+
+outputs:
+  outDir:
+    type: Directory
+    outputBinding:
+      glob: $(inputs.outDir.basename)

tests/resources/basicfl.cwl

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+#!/usr/bin/env cwl-runner
+
+cwlVersion: v1.0
+class: CommandLineTool
+
+requirements:
+  DockerRequirement:
+    dockerPull: polusai/basic-flatfield-estimation-plugin:2.1.0
+  InitialWorkDirRequirement:
+    listing:
+    - writable: true
+      entry: $(inputs.outDir)
+  InlineJavascriptRequirement: {}
+
+inputs:
+  filePattern:
+    type: string
+    inputBinding:
+      prefix: --filePattern
+  getDarkfield:
+    type: boolean
+    inputBinding:
+      prefix: --getDarkfield
+  groupBy:
+    type: string?
+    inputBinding:
+      prefix: --groupBy
+  inpDir:
+    type: Directory
+    inputBinding:
+      prefix: --inpDir
+  outDir:
+    type: Directory
+    inputBinding:
+      prefix: --outDir
+
+outputs:
+  outDir:
+    type: Directory
+    outputBinding:
+      glob: $(inputs.outDir.basename)

tests/resources/filerenaming.cwl

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+#!/usr/bin/env cwl-runner
+
+cwlVersion: v1.1
+class: CommandLineTool
+
+requirements:
+  DockerRequirement:
+    dockerPull: polusai/file-renaming-plugin:0.2.0
+  InitialWorkDirRequirement:
+    listing:
+    - writable: true
+      entry: $(inputs.outDir)
+  InlineJavascriptRequirement: {}
+
+inputs:
+  filePattern:
+    type: string
+    inputBinding:
+      prefix: --filePattern
+  inpDir:
+    type: Directory
+    inputBinding:
+      prefix: --inpDir
+  mapDirectory:
+    type: string?
+    inputBinding:
+      prefix: --mapDirectory
+  outDir:
+    type: Directory
+    inputBinding:
+      prefix: --outDir
+  outFilePattern:
+    type: string
+    inputBinding:
+      prefix: --outFilePattern
+
+outputs:
+  outDir:
+    type: Directory
+    outputBinding:
+      glob: $(inputs.outDir.basename)

tests/resources/filerenaming_io.yml

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+filePattern: .*_{row:c}{col:dd}_s{s:d}_w{channel:d}.*.ome.tif
+mapDirectory: raw
+outFilePattern: x{row:dd}_y{col:dd}_p{s:dd}_c{channel:d}.ome.tif

tests/resources/montage.cwl

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+class: CommandLineTool
+cwlVersion: v1.2
+inputs:
+  filePattern:
+    inputBinding:
+      prefix: --filePattern
+    type: string
+  flipAxis:
+    inputBinding:
+      prefix: --flipAxis
+    type: string?
+  gridSpacing:
+    inputBinding:
+      prefix: --gridSpacing
+    type: string?
+  imageSpacing:
+    inputBinding:
+      prefix: --imageSpacing
+    type: string?
+  inpDir:
+    inputBinding:
+      prefix: --inpDir
+    type: Directory
+  layout:
+    inputBinding:
+      prefix: --layout
+    type: string?
+  outDir:
+    inputBinding:
+      prefix: --outDir
+    type: Directory
+outputs:
+  outDir:
+    outputBinding:
+      glob: $(inputs.outDir.basename)
+    type: Directory
+requirements:
+  DockerRequirement:
+    dockerPull: polusai/montage-plugin:0.5.0
+  InitialWorkDirRequirement:
+    listing:
+    - entry: $(inputs.outDir)
+      writable: true
+  InlineJavascriptRequirement: {}

tests/resources/omeconverter.cwl

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+class: CommandLineTool
+cwlVersion: v1.2
+inputs:
+  fileExtension:
+    inputBinding:
+      prefix: --fileExtension
+    type: string
+  filePattern:
+    inputBinding:
+      prefix: --filePattern
+    type: string
+  inpDir:
+    inputBinding:
+      prefix: --inpDir
+    type: Directory
+  outDir:
+    inputBinding:
+      prefix: --outDir
+    type: Directory
+outputs:
+  outDir:
+    outputBinding:
+      glob: $(inputs.outDir.basename)
+    type: Directory
+requirements:
+  DockerRequirement:
+    dockerPull: polusai/ome-converter-plugin:0.3.0
+  InitialWorkDirRequirement:
+    listing:
+    - entry: $(inputs.outDir)
+      writable: true
+  InlineJavascriptRequirement: {}