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

## Documentation for package ‘sevenbridges’ version 1.20.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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

sevenbridges-package | 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