@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 .
rdfs:comment "The name of the auxillary view to be used for background subtraction. Background will be estimated if not provided." ;
cwl:inputBinding [ CommandLineBinding:prefix
"--background-view" ] ;
cwl:inputBinding [ CommandLineBinding:prefix
"--background-view" ] ;
sld:type xsd:string , sld:null .
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
rdfs:comment "Levelling method for clip and scale application. Defaults to SCALE_BY_CHUNK. If rescaling is configured in parameter_json, will be set to SCALE_BY_CHUNK if true, SCALE_BY_IMAGE if false." ;
sld:type xsd:string , sld:null .
rdfs:comment "If true, histograms will be equalized." ;
cwl:inputBinding [ CommandLineBinding:prefix
"--match-histogram" ] ;
cwl:inputBinding [ CommandLineBinding:prefix
"--match-histogram" ] ;
sld:type xsd:boolean , sld:null .
rdfs:comment "If provided, the number of processes that will be spawned for processing. Otherwise, the maximum number of available CPUs will be used." ;
cwl:inputBinding [ CommandLineBinding:prefix
"--n-processes" ] ;
cwl:inputBinding [ CommandLineBinding:prefix
"--n-processes" ] ;
sld:type xsd:int , sld:null .
sld:type xsd:string .
rdfs:comment "Sigma value for low pass gaussian filter. Will not be run if not provided." ;
cwl:inputBinding [ CommandLineBinding:prefix
"--low-sigma" ] ;
cwl:inputBinding [ CommandLineBinding:prefix
"--low-sigma" ] ;
sld:type xsd:int , sld:null .
sld:type xsd:boolean .
rdfs:comment "The name of the auxillary view to be processed in parallel with primary view, such as for anchor round in ISS processing. Will not be included if not provided." ;
cwl:inputBinding [ CommandLineBinding:prefix
"--anchor-view" ] ;
cwl:inputBinding [ CommandLineBinding:prefix
"--anchor-view" ] ;
sld:type xsd:string , sld:null .
a cwl:Workflow ;
ns1:original_cwlVersion "v1.2" ;
Workflow:steps , , , ;
cwl:cwlVersion cwl:v1.2 ;
cwl:inputs , , , , , , , , , , , , , , , , , , , , , ;
cwl:outputs ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] ;
cwl:requirements [ a cwl:MultipleInputFeatureRequirement ] ;
cwl:requirements [ a cwl:StepInputExpressionRequirement ] .
cwl:source , ;
cwl:valueFrom "${\n if(self[0]){\n return self[0];\n } else if(self[1]) {\n return self[1];\n } else {\n return null;\n }\n}\n" .
sld:type xsd:int .
rdfs:comment "The name of the auxillary view to be used for image registration." ;
sld:type xsd:string , sld:null .
rdfs:comment "Radius for white top hat filter. Should be slightly larger than the expected spot radius. Will not be run if not provided." ;
cwl:inputBinding [ CommandLineBinding:prefix
"--tophat-radius" ] ;
cwl:inputBinding [ CommandLineBinding:prefix
"--tophat-radius" ] ;
sld:type xsd:int , sld:null .
sld:type xsd:float .
sld:type xsd:int .
cwl:source , ;
cwl:valueFrom "${\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:type xsd:float .
sld:type xsd:int .
sld:type xsd:float .
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 .
sld:type xsd:int .
sld:type xsd:int .
sld:type xsd:int .
sld:type xsd:boolean .
rdfs:comment "Whether to treat the zplanes as a 3D image." ;
cwl:inputBinding [ CommandLineBinding:prefix
"--is-volume" ] ;
cwl:inputBinding [ CommandLineBinding:prefix
"--is-volume" ] ;
sld:type xsd:boolean , sld:null .
rdfs:comment "Pixels above this percentile are set to 1. Defaults to 99.9." ;
cwl:inputBinding [ CommandLineBinding:prefix
"--clip-max" ] ;
cwl:inputBinding [ CommandLineBinding:prefix
"--clip-max" ] ;
sld:type xsd:float , sld:null .
sld:type xsd:boolean .
sld:type xsd:int .
rdfs:comment "Levelling method for clip and scale application. Defaults to SCALE_BY_CHUNK." ;
cwl:inputBinding [ CommandLineBinding:prefix
"--level-method" ] ;
cwl:inputBinding [ CommandLineBinding:prefix
"--level-method" ] ;
sld:type xsd:string , sld:null .
rdfs:comment "Sigma value for deconvolution. Should be approximately the expected spot size." ;
sld:type xsd:int , sld:null .
sld:type xsd:float .
sld:type xsd:float .
sld:type [ sld:items xsd:float ;
sld:type sld:array
] .
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
cwl:out ;
cwl:run .
sld:type xsd:float .
rdfs:comment "Whether to iteratively rescale images before running the decoder. If true, will skip clip and scale at the end of this step." ;
sld:type xsd:boolean , sld:null .
sld:type xsd:int .
cwl:in ;
cwl:out ;
cwl:run [ a cwl:CommandLineTool ;
cwl:baseCommand ( "cat" ) ;
cwl:baseCommand ( "cat" ) ;
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"
] ;
cwl:stdout "cc82aa74380bb71b0de25fb486163af8ba29a2b2"
] .
sld:type xsd:string .
sld:type xsd:string .
sld:type xsd:string .
sld:type xsd:int .
sld:type xsd:boolean .
sld:type xsd:boolean .
rdfs:comment "json containing step parameters." ;
sld:type cwl:File , sld:null .
sld:type xsd:int .
rdfs:comment "The number of images associated with each channel in the registration image. Will be calculated from aux view if provided through parameter_json, otherwise defaults to one." ;
sld:type xsd:int , sld:null .
sld:type xsd:boolean .
sld:type xsd:int .
sld:type xsd:int .
sld:type [ sld:items xsd:float ;
sld:type sld:array
] .
sld:type xsd:boolean .
sld:type xsd:int .
cwl:source , ;
cwl:valueFrom "${\n if(!(self[0] === null)){\n return self[0];\n } else if(!(self[1] === null)) {\n return self[1];\n } else {\n return null;\n }\n}\n" .
rdfs:comment "Pixels above this percentile are set to 1." ;
sld:type xsd:float , sld:null .
cwl:valueFrom "/opt/processing.json" .
rdfs:comment "Whether to treat the zplanes as a 3D image." ;
sld:type xsd:boolean , sld:null .
rdfs:comment "Root directory containing space_tx formatted experiment" ;
cwl:inputBinding [ CommandLineBinding:prefix
"--input-dir" ] ;
cwl:inputBinding [ CommandLineBinding:prefix
"--input-dir" ] ;
sld:type cwl:Directory .
sld:type xsd:int .
sld:type xsd:boolean .
sld:type xsd:int .
sld:type xsd:float .
cwl:outputSource ;
sld:type cwl:Directory .
sld:type xsd:string .
cwl:outputBinding [ CommandOutputBinding:glob
"$(\"tmp/\" + inputs.tmp_prefix + \"/3_processed/\")" ] ;
cwl:outputBinding [ CommandOutputBinding:glob
"$(\"tmp/\" + inputs.tmp_prefix + \"/3_processed/\")" ] ;
sld:type cwl:Directory .
sld:type [ sld:items xsd:int ;
sld:type sld:array
] .
sld:type xsd:string .
sld:type xsd:boolean .
cwl:source , ;
cwl:valueFrom "${\n if(self[0]){\n return self[0];\n } else if(self[1]) {\n return self[1];\n } else {\n return null;\n }\n}\n" .
sld:type xsd:string .
cwl:inputBinding [ CommandLineBinding:prefix
"--tmp-prefix" ] ;
cwl:inputBinding [ CommandLineBinding:prefix
"--tmp-prefix" ] ;
sld:type xsd:string .
sld:type xsd:boolean .
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
sld:type xsd:int .
sld:type xsd:string .
cwl:source .
cwl:inputBinding [ CommandLineBinding:prefix
"--register-to-primary" ] ;
cwl:inputBinding [ CommandLineBinding:prefix
"--register-to-primary" ] ;
sld:type xsd:boolean , sld:null .
sld:type xsd:float .
sld:type xsd:string .
cwl:source , ;
cwl:valueFrom "${\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 , ;
cwl:valueFrom "${\n if(self[0]){\n return self[0];\n } else if(self[1]) {\n return self[1];\n } else {\n return null;\n }\n}\n" .
sld:type xsd:int .
rdfs:comment "Sigma value for high pass gaussian filter. Will not be run if not provided." ;
cwl:inputBinding [ CommandLineBinding:prefix
"--high-sigma" ] ;
cwl:inputBinding [ CommandLineBinding:prefix
"--high-sigma" ] ;
sld:type xsd:int , sld:null .
cwl:inputBinding [ cwl:loadContents true ] ;
sld:type cwl:File .
sld:type xsd:string .
cwl:outputBinding [ CommandOutputBinding:glob
"cc82aa74380bb71b0de25fb486163af8ba29a2b2" ] ;
cwl:outputBinding [ CommandOutputBinding:glob
"cc82aa74380bb71b0de25fb486163af8ba29a2b2" ] ;
sld:type cwl:File .
sld:type xsd:float .
sld:type xsd:boolean .
sld:type xsd:float .
cwl:source , ;
cwl:valueFrom "${\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:type xsd:boolean .
sld:type xsd:boolean .
sld:type xsd:int .
sld:type xsd:int .
sld:type xsd:int .
rdfs:comment "Radius for white top hat filter. Should be slightly larger than the expected spot radius. Will not be run if not provided." ;
sld:type xsd:int , sld:null .
cwl:inputBinding [ CommandLineBinding:position
1 ] ;
cwl:inputBinding [ CommandLineBinding:position
1 ] ;
sld:type xsd:string .
sld:type xsd:string .
rdfs:comment "Root directory containing space_tx formatted experiment" ;
sld:type cwl:Directory .
cwl:source , ;
cwl:valueFrom "${\n if(self[0]){\n return self[0];\n } else if(self[1]) {\n return self[1];\n } else {\n return null;\n }\n}\n" .
rdfs:comment "If true, the `background_view` will be aligned to the `aux_view`." ;
sld:type xsd:boolean , sld:null .
rdfs:comment "Radius for rolling ball background subtraction. Larger values lead to increased intensity evening effect. The value of 3 will work for most datasets. Will not be run if not provided." ;
cwl:inputBinding [ CommandLineBinding:prefix
"--rolling-radius" ] ;
cwl:inputBinding [ CommandLineBinding:prefix
"--rolling-radius" ] ;
sld:type xsd:int , sld:null .
cwl:source , , , , , , ;
cwl:valueFrom "${\n if (self[1]){\n return self[1];\n } else if (self[2] && self[5] && self[6]) {\n var name = \"\";\n if(self[3]){\n name = self[3];\n } else {\n name = self[4];\n }\n var aux_ind = self[5].indexOf(name);\n var aux_count = self[6][aux_ind];\n return Math.round(self[2] / aux_count);\n } else if(self[0]){\n return self[0];\n } else {\n return null;\n }\n}\n" .
rdfs:comment "The name of the auxillary view to be used for image registration. Registration will not be performed if not provided." ;
cwl:inputBinding [ CommandLineBinding:prefix
"--register-aux-view" ] ;
cwl:inputBinding [ CommandLineBinding:prefix
"--register-aux-view" ] ;
sld:type xsd:string , sld:null .
sld:type xsd:int .
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:type xsd:string .
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
sld:type xsd:int .
sld:type xsd:int .
rdfs:comment "Sigma value for deconvolution. Should be approximately the expected spot size." ;
cwl:inputBinding [ CommandLineBinding:prefix
"--decon-sigma" ] ;
cwl:inputBinding [ CommandLineBinding:prefix
"--decon-sigma" ] ;
sld:type xsd:int , sld:null .
rdfs:comment "Number of iterations to perform for deconvolution. High values remove more noise while lower values remove less. The value 15 will work for most datasets unless image is very noisy. Will not be run if not provided." ;
cwl:inputBinding [ CommandLineBinding:prefix
"--decon-iter" ] ;
cwl:inputBinding [ CommandLineBinding:prefix
"--decon-iter" ] ;
sld:type xsd:int , sld:null .
sld:type xsd:float .
rdfs:comment "Sigma value for low pass gaussian filter. Will not be run if not provided." ;
sld:type xsd:int , sld:null .
sld:type xsd:boolean .
rdfs:comment "If true, the `background_view` will be aligned to the `aux_name`." ;
cwl:inputBinding [ CommandLineBinding:prefix
"--register-background" ] ;
cwl:inputBinding [ CommandLineBinding:prefix
"--register-background" ] ;
sld:type xsd:boolean , sld:null .
sld:type xsd:float .
sld:type xsd:boolean .
sld:type xsd:string .
sld:type xsd:int .
sld:type xsd:int .
rdfs:comment "The name of the auxillary view to be used for background subtraction. Background will be estimated if not provided." ;
sld:type xsd:string , sld:null .
rdfs:comment "The number of images associated with each channel of the registration image. Defaults to 1." ;
cwl:inputBinding [ CommandLineBinding:prefix
"--ch-per-reg" ] ;
cwl:inputBinding [ CommandLineBinding:prefix
"--ch-per-reg" ] ;
sld:type xsd:int , sld:null .
sld:type xsd:int .
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
sld:type xsd:string .
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
rdfs:comment "If true, histograms will be equalized." ;
sld:type xsd:boolean , 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:type xsd:float .
sld:type xsd:boolean .
cwl:source , ;
cwl:valueFrom "${\n if(self[0]){\n return self[0];\n } else if(self[1]) {\n return self[1];\n } else {\n return null;\n }\n}\n" .
sld:type xsd:int .
rdfs:comment "If true, registration will be performed between the first round of register_aux_view and the primary images." ;
sld:type xsd:boolean , sld:null .
sld:type xsd:boolean .
sld:type xsd:float .
cwl:source , ;
cwl:valueFrom "${\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:type [ sld:items xsd:string ;
sld:type sld:array
] .
sld:type xsd:float .
sld:type xsd:int .
cwl:source , ;
cwl:valueFrom "${\n if(self[0]){\n return self[0];\n } else if(self[1]) {\n return self[1];\n } else {\n return null;\n }\n}\n" .
sld:type xsd:int .
cwl:source .
a cwl:ExpressionTool ;
ns1:original_cwlVersion "v1.0" ;
ExpressionTool:expression "${ var data = JSON.parse(inputs.datafile.contents);\n var schema = JSON.parse(inputs.schema.contents);\n function enforce_record(data, key, items, output_dict){\n if(Array.isArray(items[0])){\n // Record where one of a mutually exclusive set of sublists is defined\n // Find closest match and enforce that\n var subind = 0;\n var coverage = 0.0;\n for(var i=0;i coverage){\n coverage = new_coverage;\n subind = i;\n }\n }\n enforce_record(data, key, items[subind], output_dict);\n } else {\n for(var i=0;i , ;
cwl:outputs , , , , , , , , , , , , , , , , , , , , , , , ,