test_tool_cwlrun: Test tools with cwl-runner

Description Usage Arguments Value Examples

View source: R/api-utils.R

Description

Test tools locally cwl-runner (https://github.com/common-workflow-language/cwltool)

Usage

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test_tool_cwlrun(rabix_tool, inputs = list())

Arguments

rabix_tool

rabix tool from Tool class

inputs

input parameters declared as json (or yaml) string

Value

cwl-runner stdout

Examples

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## Not run: 
inputs <- '{"counts_file": {"class": "File", "path": "./FPKM.txt"}, "gene_names": "BRCA1"}'
rbx <- <define rabix tool>
set_test_env("tengfei/testenv", "<mount_dir>")
test_tool_cwlrun(rbx, inputs)

## End(Not run)

tengfei/sevenbridges documentation built on March 27, 2021, 1:22 p.m.