added ict and clts

utils/omero-download-tool/ict.yaml

@@ -0,0 +1,68 @@
+author:
+- Hamdah Shafqat
+contact: [email protected]
+container: polusai/omero-download-tool:0.1.0-dev0
+description: This plugin allows to retrieve the microscopy image data from the OMERO
+  NCATS server.
+entrypoint: python3 -m polus.images.utils.omero_download
+inputs:
+- description: The supported object types to be retreived.
+  format:
+  - dataType
+  name: dataType
+  required: true
+  type: string
+- description: Name of the object to be downloaded.
+  format:
+  - name
+  name: name
+  required: false
+  type: string
+- description: Identifier of the object to be downloaded.
+  format:
+  - objectId
+  name: objectId
+  required: false
+  type: number
+- description: Generate an output preview.
+  format:
+  - preview
+  name: preview
+  required: false
+  type: boolean
+name: polusai/OmeroDownload
+outputs:
+- description: Output collection.
+  format:
+  - outDir
+  name: outDir
+  required: true
+  type: path
+repository: https://github.com/PolusAI/image-tools
+specVersion: 1.0.0
+title: Omero Download
+ui:
+- description: The supported object types to be retreived.
+  fields:
+  - project
+  - dataset
+  - screen
+  - plate
+  - well
+  - default
+  key: inputs.dataType
+  title: dataType
+  type: select
+- description: Name of the object to be downloaded.
+  key: inputs.name
+  title: name
+  type: text
+- description: Identifier of the object to be downloaded.
+  key: inputs.objectId
+  title: objectId
+  type: number
+- description: Generate an output preview.
+  key: inputs.preview
+  title: Preview example output of this plugin
+  type: checkbox
+version: 0.1.0-dev0

utils/omero-download-tool/omerodownload.cwl

@@ -0,0 +1,36 @@
+class: CommandLineTool
+cwlVersion: v1.2
+inputs:
+  dataType:
+    inputBinding:
+      prefix: --dataType
+    type: string
+  name:
+    inputBinding:
+      prefix: --name
+    type: string?
+  objectId:
+    inputBinding:
+      prefix: --objectId
+    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/omero-download-tool:0.1.0-dev0
+  InitialWorkDirRequirement:
+    listing:
+    - entry: $(inputs.outDir)
+      writable: true
+  InlineJavascriptRequirement: {}

utils/omero-download-tool/plugin.json

@@ -1,14 +1,14 @@
 {
   "name": "Omero Download",
   "version": "0.1.0-dev0",
-  "title": "Retrieve data from the OMERO NCATS server",
+  "containerId": "polusai/omero-download-tool:0.1.0-dev0",
+  "title": "Omero Download",
   "description": "This plugin allows to retrieve the microscopy image data from the OMERO NCATS server.",
   "author": "Hamdah Shafqat Abbasi ([email protected])",
   "institution": "National Center for Advancing Translational Sciences, National Institutes of Health",
   "repository": "https://github.com/PolusAI/image-tools",
   "website": "https://ncats.nih.gov/preclinical/core/informatics",
   "citation": "",
-  "containerId": "polusai/omero-download-tool:0.1.0-dev0",
   "baseCommand": [
     "python3",
     "-m",