## It will check the SYSargs class and methods
skip_on_bioc()
skip_on_ci()
## It will check the cmd2cwl class and methods
library(systemPipeR)
test_that("check_LineWise_test", {
## build simple example
command <- "
hisat2 \
-S <F, out: ./results/M1A.sam> \
-x <F: ./data/tair10.fasta> \
-k <int: 1> \
-min-intronlen <int: 30> \
-max-intronlen <int: 3000> \
-threads <int: 4> \
-U <F: ./data/SRR446027_1.fastq.gz>
"
cmd <- createParamFiles(command, writeParamFiles = FALSE)
expect_s4_class(cmd, "SYSargs2")
writeParamFiles(cmd, overwrite = TRUE)
expect_true(file.exists("param/cwl/hisat2/hisat2.yml"))
expect_true(file.exists("param/cwl/hisat2/hisat2.cwl"))
## printParam
print_cmd <- printParam(cmd, position = "baseCommand")
expect_s3_class(print_cmd, "cwlParse")
## subsetParam
cmd2 <- subsetParam(cmd, position = "inputs", index = 1, trim = TRUE)
expect_equal(cmdlist(cmd2)[[1]][[1]], "hisat2 -S ./results/M1A.sam")
## renameParam
cmd3 <- renameParam(cmd, "input", index = 1, rename = "sam")
expect_equal(names(cmd3$cmdToCwl$inputs)[1], "sam")
## replaceParam
new_inputs <- new_inputs <- list(
"new_input1" = list(type = "File", preF = "-b", yml = "myfile"),
"new_input2" = "-L <int: 4>"
)
cmd4 <- replaceParam(cmd, "inputs", index = 1:2, replace = new_inputs)
expect_equal(names(cmd4$cmdToCwl$inputs)[1], "new_input1")
## appendParam
newIn <- new_inputs <- list(
"new_input1" = list(type = "File", preF = "-b1", yml = "myfile1"),
"new_input2" = list(type = "File", preF = "-b2", yml = "myfile2"),
"new_input3" = "-b3 <F: myfile3>"
)
cmd5 <- appendParam(cmd, "inputs", index = 1:2, append = new_inputs)
expect_equal(names(cmd5$cmdToCwl$inputs)[10], "new_input3")
})
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