Seven Bridges Platform API Client and Common Workflow Language Tool Builder in R

Documentation for package ‘sevenbridges’ version 1.38.0

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A B C D E F G H I L M O P Q R S T U V W misc

Seven Bridges Platform API Client and CWL Tool Builder in R

-- A --

access_level	Meta schema
addIdNum	add '#' prefix to id
add_tag	Set file tags
add_tag-method	Set file tags
age_at_diagnosis	Meta schema
aliquot_id	Meta schema
aliquot_uuid	Meta schema
analysis_uuid	Meta schema
anyReq	Rabix specifc Requirements
AnyRequirement	Rabix specifc Requirements
AnyRequirement-class	Rabix specifc Requirements
api	Core HTTP logic for Seven Bridges API
App	Class App
App-class	Class App
appType	Convert App or a CWL JSON file to Tool or Flow object
argslist	Shorthand functions for cwl packages constructors
asList	Convert a object slots/fields to a list, json, or yaml file
asList-method	Convert a object slots/fields to a list, json, or yaml file
Auth	Class Auth
Auth-class	Class Auth
aws	Rabix specifc Requirements
AWSInstanceTypeRequirement	Rabix specifc Requirements
AWSInstanceTypeRequirement-class	Rabix specifc Requirements

-- B --

batch	batch function for task batch execution
Binding	Binding
Binding-class	Binding

-- C --

case_id	Meta schema
case_uuid	Meta schema
CCBList	characterORCommandLineBindingList Class
characterORCommandLineBindingList-class	characterORCommandLineBindingList Class
CLB	Shorthand functions for cwl packages constructors
cli_list_projects	List projects using Seven Bridges command line uploader
cli_list_tags	List all the tags in project using Seven Bridges command line uploader
cli_upload	Upload files using Seven Bridges command line uploader
COB	Shorthand functions for cwl packages constructors
CommandInputParameter	CommandInputParameter Class
CommandInputParameter-class	CommandInputParameter Class
CommandInputSchema	CommandInputSchema Class
CommandInputSchema-class	CommandInputSchema Class
CommandLineBinding	CommandLineBinding Class
CommandLineBinding-class	CommandLineBinding Class
CommandLineTool	CommandLineTool Class
CommandLineTool-class	CommandLineTool Class
CommandOutputBinding	CommandOutputBinding Class
CommandOutputBinding-class	CommandOutputBinding Class
CommandOutputParameter	CommandOutputParameter Class
CommandOutputParameter-class	CommandOutputParameter Class
CommandOutputSchema	CommandOutputSchema
CommandOutputSchema-class	CommandOutputSchema
ComplexEnum	Pre-defiend enums
ComplexSingleEnum-class	Pre-defiend enums
convert_app	Convert App or a CWL JSON file to Tool or Flow object
cpu	Rabix specifc Requirements
CPURequirement	Rabix specifc Requirements
CPURequirement-class	Rabix specifc Requirements
CreateFileRequirement	ProcessRequirement Class
CreateFileRequirement-class	ProcessRequirement Class
CWL	Class CWL
CWL-class	Class CWL

-- D --

DatatypeEnum	Pre-defiend enums
DatatypeSingleEnum-class	Pre-defiend enums
data_format	Meta schema
data_subtype	Meta schema
data_type	Meta schema
days_to_death	Meta schema
delete	Delete files or folders
delete-method	Delete files or folders
disease_type	Meta schema
docker	Rabix specifc Requirements
DockerRequirement	ProcessRequirement Class
DockerRequirement-class	ProcessRequirement Class
download	Download files
download-method	Download files
DSCList	DSC list
DSCList-class	DSC list

-- E --

enum	Pre-defiend enums
enum-class	Pre-defiend enums
EnvironmentDef	ProcessRequirement Class
EnvironmentDef-class	ProcessRequirement Class
EnvironmentDefList	ProcessRequirement Class
EnvironmentDefList-class	ProcessRequirement Class
EnvVarRequirement	ProcessRequirement Class
EnvVarRequirement-class	ProcessRequirement Class
ethnicity	Meta schema
experimental_strategy	Meta schema
Expression	Expression Class
Expression-class	Expression Class
ExpressionEngineRequirement	ProcessRequirement Class
ExpressionEngineRequirement-class	ProcessRequirement Class
ExpressionTool	ExpressionTool Class
ExpressionTool-class	ExpressionTool Class

-- F --

File	FileList Class
File-class	FileList Class
FileDef	ProcessRequirement Class
fileDef	Rabix specifc Requirements
FileDef-class	ProcessRequirement Class
FileDefList	ProcessRequirement Class
FileDefList-class	ProcessRequirement Class
FileList	FileList Class
FileList-class	FileList Class
Files	Class Files
Files-class	Class Files
FilesList	Class Files
FilesList-class	Class Files
file_extension	Meta schema
file_segment_number	Meta schema
Flow	Build workflow
FS	FS class
FS-class	FS class

-- G --

gdc_file_uuid	Meta schema
gender	Meta schema
getTaskHook	set task function hook
get_cwl_class	Get class from CWL JSON file
get_token	Opens web browser to copy the auth token
get_uploader	Download Seven Bridges command line uploader and extract to a specified directory

-- H --

Handler	Handler instance
Handler-class	Handler instance

-- I --

InPar	Shorthand functions for cwl packages constructors
input	Shorthand functions for cwl packages constructors
InputParameter	Paramter class (reference class)
InputParameter-class	Paramter class (reference class)
InputParameterList	Paramter class (reference class)
InputParameterList-class	Paramter class (reference class)
InputSchema	SchemaList
InputSchema-class	SchemaList
input_matrix	Get input/output matrix out of JSON CWL file directly
investigation	Meta schema
IPList	Shorthand functions for cwl packages constructors
is_commandlinetool	Get class from CWL JSON file
is_workflow	Get class from CWL JSON file
Item	Class Item
Item-class	Class Item
ItemArray	Pre-defiend enums
ItemArray-class	Pre-defiend enums

-- L --

library_id	Meta schema
link	link two nodes to form a new Workflow
link-method	link two nodes to form a new Workflow
link_what	List possible linking methods
link_what-method	List possible linking methods

-- M --

mem	Rabix specifc Requirements
MemRequirement	Rabix specifc Requirements
MemRequirement-class	Rabix specifc Requirements
Metadata	Meta schema
Metadata-class	Meta schema
misc_get_token	Opens web browser to copy the auth token
misc_get_uploader	Download Seven Bridges command line uploader and extract to a specified directory
misc_make_metadata	Meta schema
misc_upload_cli	Upload files using Seven Bridges command line uploader

-- O --

OPList	Shorthand functions for cwl packages constructors
OutPar	Shorthand functions for cwl packages constructors
output	Shorthand functions for cwl packages constructors
OutputParameter	Paramter class (reference class)
OutputParameter-class	Paramter class (reference class)
OutputParameterList	Paramter class (reference class)
OutputParameterList-class	Paramter class (reference class)
OutputSchema	SchemaList
OutputSchema-class	SchemaList
output_matrix	Get input/output matrix out of JSON CWL file directly

-- P --

paired_end	Meta schema
Parameter	Paramter class (reference class)
Parameter-class	Paramter class (reference class)
platform	Meta schema
platform_unit_id	Meta schema
primary_site	Meta schema
PrimitiveEnum	Pre-defiend enums
PrimitiveSingleEnum-class	Pre-defiend enums
Process	Process Class
Process-class	Process Class
ProcessRequirement	ProcessRequirement Class
ProcessRequirement-class	ProcessRequirement Class
ProcessRequirementList	ProcessRequirement Class
ProcessRequirementList-class	ProcessRequirement Class
project_details	Returns the details of the project
project_members	Returns a list of all users invited to the project and their privileges

-- Q --

quality_scale

Meta schema

-- R --

race	Meta schema
reference_genome	Meta schema
requirements	Rabix specifc Requirements
response	Get raw response from an Item object
response-method	Get raw response from an Item object
response<-	Get raw response from an Item object
response<--method	Get raw response from an Item object

-- S --

sample_id	Meta schema
sample_type	Meta schema
sample_uuid	Meta schema
SBGWorkflow	Build workflow
SBGWorkflow-class	Build workflow
sbg_get_env	Set authentication environment variables for Seven Bridges API
sbg_set_env	Set authentication environment variables for Seven Bridges API
ScatterFeatureRequirement	ProcessRequirement Class
ScatterFeatureRequirement-class	ProcessRequirement Class
ScehmaList	SchemaList
Schema	SchemaList
Schema-class	SchemaList
SchemaDef	SchemaList
SchemaDef-class	SchemaList
SchemaDefList	SchemaList
SchemaDefList-class	SchemaList
SchemaList	SchemaList
SchemaList-class	SchemaList
setListClass	List Class generator.
setTaskHook	set task function hook
set_tag	Set file tags
set_tag-method	Set file tags
set_test_env	Set testing env
SubworkflowFeatureRequirement	ProcessRequirement Class
SubworkflowFeatureRequirement-class	ProcessRequirement Class

-- T --

test_tool_bunny	Test tools in rabix/bunny
test_tool_cwlrun	Test tools with cwl-runner
test_tool_rabix	Test tools in rabix/rabix-devel (DEPRECATED)
Tool	Class Tool
Tool-class	Class Tool

-- U --

upload_complete_all	Reports the complete file upload
upload_complete_part	Reports the completion of the part upload
upload_delete	Abort the upload
upload_info	Returns upload information for the ongoing upload
upload_info_part	Returns AWS S3 signed URL for a part of the file upload
upload_init	Initializes the upload of the specified file

-- V --

vital_status

Meta schema

-- W --

Workflow	Workflow
Workflow-class	Workflow
WorkflowOutputParameter	Workflow
WorkflowOutputParameter-class	Workflow
WorkflowOutputParameterList	Workflow
WorkflowOutputParameterList-class	Workflow
WorkflowStep	WorkflowStepInputList
WorkflowStep-class	WorkflowStepInputList
WorkflowStepInput	WorkflowStepInputList
WorkflowStepInput-class	WorkflowStepInputList
WorkflowStepInputList	WorkflowStepInputList
WorkflowStepInputList-class	WorkflowStepInputList
WorkflowStepList	WorkflowStepInputList
WorkflowStepList-class	WorkflowStepInputList
WorkflowStepOutput	WorkflowStepInputList
WorkflowStepOutput-class	WorkflowStepInputList
WorkflowStepOutputList	WorkflowStepInputList
WorkflowStepOutputList-class	WorkflowStepInputList

-- misc --

"%>>%"	Build workflow
"%>>%"-method	Build workflow
"+"-method	Build workflow
%>>%	Build workflow
%>>%-method	Build workflow
+-method	Build workflow