@prefix NetworkAccess: .
@prefix rdf: .
@prefix CommandLineBinding: .
@prefix xsd: .
@prefix DockerRequirement: .
@prefix Workflow: .
@prefix cwl: .
@prefix sld: .
@prefix rdfs: .
@prefix CommandOutputBinding: .
@prefix ns1: .
@prefix ExpressionTool: .
sld:type xsd:float .
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
sld:type xsd:string .
sld:type xsd:boolean .
cwl:source , , , , , , , , , , , , , , , , , ;
cwl:valueFrom "${\n if(self[14] && self[15]) {\n return {\n \"roi_set\": self[14],\n \"file_formats\": self[15]\n }\n } else if(self[16] && self[17]){\n return {\n \"labeled_image\": self[16],\n \"file_formats_labeled\": self[17]\n };\n } else if(!self[1] && !self[6]){\n return self[0];\n } else if(self[1]){\n return {\n \"img_threshold\": self[1],\n \"min_dist\": self[2],\n \"min_allowed_size\": self[3],\n \"max_allowed_size\": self[4],\n \"masking_radius\": self[5]\n };\n } else {\n return {\n \"nuclei_view\": self[6],\n \"cyto_seg\": self[7],\n \"correct_seg\": self[8],\n \"border_buffer\": self[9],\n \"area_thresh\": self[10],\n \"thresh_block_size\": self[11],\n \"watershed_footprint_size\": self[12],\n \"label_exp_size\": self[13]\n };\n }\n}\n" .
cwl:source .
sld:fields , , , , , , , ;
sld:type sld:record .
rdfs:comment "Flattened file input, refer to record entry \"binary_mask\"" ;
sld:type cwl:Directory , sld:null .
sld:fields , , , , , , , ;
sld:type sld:record .
sld:type xsd:int .
cwl:inputBinding [ CommandLineBinding:prefix
"--cyto-seg" ] ;
cwl:inputBinding [ CommandLineBinding:prefix
"--cyto-seg" ] ;
sld:type xsd:boolean .
rdfs:comment "If true, the cytoplasm will be segmented" ;
sld:type xsd:boolean .
rdfs:comment "If true, suspected nuclei/cytoplasms that overlap will be removed." ;
sld:type xsd:boolean .
cwl:outputBinding [ CommandOutputBinding:glob
"$(\"tmp/\" + inputs.tmp_prefix + \"/5_Segmented/\")" ] ;
cwl:outputBinding [ CommandOutputBinding:glob
"$(\"tmp/\" + inputs.tmp_prefix + \"/5_Segmented/\")" ] ;
sld:type cwl:Directory .
sld:type xsd:float .
rdfs:comment "Layout for name of each RoiSet.zip, per fov. Will be formatted with String.format([fov index])." ;
sld:type xsd:string .
rdfs:comment "Radius for white tophat noise filter" ;
sld:type xsd:int .
sld:type xsd:int .
sld:type xsd:float .
sld:type xsd:int .
sld:type xsd:float .
sld:type xsd:int .
sld:type xsd:int .
sld:type xsd:int .
sld:type xsd:boolean .
cwl:inputBinding [ CommandLineBinding:prefix
"--aux-name" ] ;
cwl:inputBinding [ CommandLineBinding:prefix
"--aux-name" ] ;
sld:type xsd:string , sld:null .
sld:type xsd:boolean .
sld:type xsd:int .
cwl:inputBinding [ CommandLineBinding:prefix
"--watershed-footprint-size" ] ;
cwl:inputBinding [ CommandLineBinding:prefix
"--watershed-footprint-size" ] ;
sld:type xsd:int .
rdfs:comment "Location of directory containing the 'experiment.json' file" ;
sld:type cwl:Directory .
sld:type , , , , sld:null .
sld:type xsd:float .
cwl:source .
cwl:inputBinding [ CommandLineBinding:prefix
"--nuclei-view" ] ;
cwl:inputBinding [ CommandLineBinding:prefix
"--nuclei-view" ] ;
sld:type xsd:string .
rdfs:comment "Directory of labeled images with image segmentation data, such as from ilastik classification." ;
sld:type cwl:Directory .
sld:type xsd:float .
sld:type [ sld:items xsd:float ;
sld:type sld:array
] .
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
sld:fields , ;
sld:type sld:record .
sld:type xsd:float .
sld:type xsd:int .
cwl:valueFrom "/opt/segmentation.json" .
sld:type xsd:string .
sld:type xsd:string .
sld:type xsd:string .
sld:type xsd:int .
sld:type xsd:boolean .
sld:type , , , .
sld:type xsd:boolean .
cwl:source .
sld:type xsd:int .
cwl:inputBinding [ CommandLineBinding:prefix
"--tmp-prefix" ] ;
cwl:inputBinding [ CommandLineBinding:prefix
"--tmp-prefix" ] ;
sld:type xsd:string .
cwl:in , , , , , ;
cwl:out ;
cwl:run [ a cwl:CommandLineTool ;
cwl:baseCommand ( "/opt/segmentationDriver.py" ) ;
cwl:baseCommand ( "/opt/segmentationDriver.py" ) ;
cwl:inputs , , , , , ;
cwl:outputs ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "hubmap/starfish-custom:latest"
] ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "hubmap/starfish-custom:latest"
]
] .
sld:type xsd:boolean .
sld:type xsd:int .
rdfs:comment "Threshold used when determining if an object is one nucleus or two or more overlapping nuclei. Objects whose ratio of convex hull area to normal area are above this threshold are removed if the option to remove overlapping nuclei is set." ;
sld:type xsd:float .
sld:type xsd:int .
sld:type [ sld:items xsd:float ;
sld:type sld:array
] .
rdfs:comment "maxiumum size for a cell (in pixels)" ;
sld:type xsd:int .
sld:type xsd:boolean .
cwl:source , ;
cwl:valueFrom "${\n if(self[0]){\n return self[0];\n } else if (self[1]){\n return self[1];\n } else {\n return null;\n }\n}\n" .
cwl:source .
rdfs:comment "If provided, segmentation will only be run on FOVs with these indices." ;
sld:type sld:null ;
sld:type [ sld:items xsd:int ;
sld:type sld:array
] .
sld:type xsd:int .
rdfs:comment "If not None, removes cytoplasms whose nuclei lie within the given distance from the border." ;
sld:type xsd:int .
cwl:in , ;
cwl:out , , , , , , , , , , , , , , ;
cwl:run ;
cwl:when "$(inputs.datafile != null)" .
cwl:inputBinding [ CommandLineBinding:prefix
"--thresh-block-size" ] ;
cwl:inputBinding [ CommandLineBinding:prefix
"--thresh-block-size" ] ;
sld:type xsd:int .
sld:type xsd:int .
sld:type xsd:boolean .
cwl:inputBinding [ CommandLineBinding:prefix
"--min-dist" ] ;
cwl:inputBinding [ CommandLineBinding:prefix
"--min-dist" ] ;
sld:type xsd:int .
rdfs:comment "minimum size for a cell (in pixels)" ;
sld:type xsd:int .
rdfs:comment "Global threshold value for images" ;
sld:type xsd:float .
sld:type xsd:int .
sld:type xsd:float .
sld:type xsd:string .
sld:type [ sld:items xsd:int ;
sld:type sld:array
] .
sld:type xsd:string .
sld:type xsd:boolean .
sld:type xsd:string .
sld:type xsd:boolean .
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
sld:type xsd:int .
sld:type xsd:string .
rdfs:comment "Layout for name of each labelled image. Will be formatted with String.format([fov index])" ;
sld:type xsd:string .
sld:type xsd:float .
cwl:inputBinding [ CommandLineBinding:prefix
"--max-size" ] ;
cwl:inputBinding [ CommandLineBinding:prefix
"--max-size" ] ;
sld:type xsd:int .
sld:type xsd:string .
sld:type xsd:int .
cwl:inputBinding [ cwl:loadContents true ] ;
sld:type cwl:File .
sld:type xsd:string .
sld:type xsd:float .
sld:type xsd:boolean .
sld:type xsd:float .
sld:type xsd:boolean .
sld:type xsd:boolean .
cwl:inputBinding [ CommandLineBinding:prefix
"--img-threshold" ] ;
cwl:inputBinding [ CommandLineBinding:prefix
"--img-threshold" ] ;
sld:type xsd:float .
sld:type xsd:int .
cwl:inputBinding [ CommandLineBinding:prefix
"--masking-radius" ] ;
cwl:inputBinding [ CommandLineBinding:prefix
"--masking-radius" ] ;
sld:type xsd:int .
rdfs:comment "Flattened record input, refer to record entry \"binary_mask\"" ;
sld:type xsd:string , sld:null .
rdfs:comment "Flattened directory input, refer to record entry \"binary_mask\"" ;
sld:type cwl:Directory , sld:null .
sld:type xsd:int .
cwl:source , ;
cwl:valueFrom "${\n if(self[0]){\n return self[0];\n } else if(self[1]) {\n return self[1];\n } else {\n return null;\n }\n}\n" .
sld:fields , ;
sld:type sld:record .
rdfs:comment "Name of the auxillary view with nuclei data" ;
sld:type xsd:string .
cwl:inputBinding [ CommandLineBinding:prefix
"--min-size" ] ;
cwl:inputBinding [ CommandLineBinding:prefix
"--min-size" ] ;
sld:type xsd:int .
sld:type xsd:int .
sld:fields , ;
sld:type sld:record .
cwl:outputSource ;
sld:type cwl:Directory .
sld:type xsd:string .
sld:type xsd:int .
rdfs:comment "If provided, processing will only be run on FOVs with these indices." ;
cwl:inputBinding [ CommandLineBinding:prefix
"--selected-fovs" ] ;
cwl:inputBinding [ CommandLineBinding:prefix
"--selected-fovs" ] ;
sld:type sld:null ;
sld:type [ sld:items xsd:int ;
sld:type sld:array
] ;
sld:type [ sld:items xsd:int ;
sld:type sld:array
] .
a cwl:ExpressionTool ;
ns1:original_cwlVersion "v1.2" ;
ExpressionTool:expression "${\n const characters = 'ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz0123456789';\n const charactersLength = characters.length;\n let counter = 0;\n let result = \"\";\n while (counter < 10) {\n result += characters.charAt(Math.floor(Math.random() * charactersLength));\n counter += 1;\n }\n return {\"tmp\": result};\n}\n" ;
cwl:cwlVersion cwl:v1.2 ;
cwl:outputs ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] .
sld:fields , , , , ;
sld:type sld:record .
sld:type xsd:string .
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
sld:type xsd:int .
sld:type xsd:int .
cwl:inputBinding [ CommandLineBinding:prefix
"--file-formats" ] ;
cwl:inputBinding [ CommandLineBinding:prefix
"--file-formats" ] ;
sld:type xsd:string .
rdfs:comment "Size of structuring element for local thresholding of nuclei. If nuclei interiors aren't passing threshold, increase this value, if too much non-nuclei is passing threshold, lower it." ;
sld:type xsd:int .
a cwl:Workflow ;
ns1:original_cwlVersion "v1.2" ;
Workflow:steps , , , ;
cwl:cwlVersion cwl:v1.2 ;
cwl:inputs , , , , , , , , , ;
cwl:outputs ;
cwl:requirements [ a cwl:StepInputExpressionRequirement ] ;
cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] ;
cwl:requirements [ a cwl:MultipleInputFeatureRequirement ] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] .
sld:fields , , , , ;
sld:type sld:record .
sld:type xsd:float .
cwl:inputBinding [ CommandLineBinding:prefix
"--file-formats-labeled" ] ;
cwl:inputBinding [ CommandLineBinding:prefix
"--file-formats-labeled" ] ;
sld:type xsd:string .
sld:type xsd:boolean .
sld:type xsd:float .
sld:type xsd:boolean .
sld:type xsd:int .
sld:type xsd:string .
sld:type xsd:int .
sld:type xsd:int .
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
cwl:outputBinding [ CommandOutputBinding:glob
"583302721336ae9533b64427af4960f1f37515ae" ] ;
cwl:outputBinding [ CommandOutputBinding:glob
"583302721336ae9533b64427af4960f1f37515ae" ] ;
sld:type cwl:File .