Function reference • sevenbridges

All functions

App-class: Class App

Auth-class: Class Auth

Binding-class: Binding

CCBList(): characterORCommandLineBindingList Class

CWL-class: Class CWL

CommandInputParameter-class: CommandInputParameter Class

CommandInputSchema-class: CommandInputSchema Class

CommandLineBinding-class: CommandLineBinding Class

CommandLineTool-class: CommandLineTool Class

CommandOutputBinding-class: CommandOutputBinding Class

CommandOutputParameter-class: CommandOutputParameter Class

CommandOutputSchema-class: CommandOutputSchema

DSCList(): DSC list

PrimitiveSingleEnum-class: Pre-defiend enums

Expression-class: Expression Class

ExpressionTool-class: ExpressionTool Class

FS-class: FS class

FileList(): FileList Class

FilesList(): Class Files

Flow() `+`(<Tool>,<Tool>) `+`(<WorkflowStepList>,<Tool>) `+`(<WorkflowStepList>,<WorkflowStepList>) `+`(<App>,<App>) `+`(<WorkflowStepList>,<App>) `%>>%`: Build workflow

Handler-class: Handler instance

Item-class: Class Item

misc_make_metadata(): Meta schema

InputParameterList() OutputParameterList(): Paramter class (reference class)

Process-class: Process Class

FileDefList() EnvironmentDefList() ProcessRequirementList(): ProcessRequirement Class

SchemaList() SchemaDefList(): SchemaList

setTaskHook() getTaskHook(): set task function hook

Tool-class: Class Tool

WorkflowOutputParameterList(): Workflow

WorkflowStepInputList() WorkflowStepOutputList() WorkflowStepList(): WorkflowStepInputList

addIdNum(): add # prefix to id

api(): Core HTTP logic for Seven Bridges API

asList(): Convert a object slots/fields to a list, json, or yaml file

batch(): batch function for task batch execution

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() misc_upload_cli(): Upload files using Seven Bridges command line uploader

convert_app() appType(): Convert App or a CWL JSON file to Tool or Flow object

get_cwl_class(): Get class from CWL JSON file

delete(): Delete files or folders

download(): Download files

get_token() misc_get_token(): Opens web browser to copy the auth token

get_uploader() misc_get_uploader(): Download Seven Bridges command line uploader and extract to a specified directory

input_matrix() output_matrix(): Get input/output matrix out of JSON CWL file directly

link(): link two nodes to form a new Workflow

link_what(): List possible linking methods

project_details(): Returns the details of the project

project_members(): Returns a list of all users invited to the project and their privileges

docker() requirements() fileDef(): Rabix specifc Requirements

response() `response<-`(): Get raw response from an Item object

sbg_get_env(): Set authentication environment variables for Seven Bridges API

sbg_set_env(): Set authentication environment variables for Seven Bridges API

setListClass(): List Class generator.

set_test_env(): Set testing env

sevenbridges-package: Seven Bridges Platform API Client and CWL Tool Builder in R

CLB: Shorthand functions for cwl packages constructors

set_tag() add_tag(): Set file tags

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)

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