ParamFiles: Accessories function to modify the Command-line Version 1

In tgirke/systemPipeR: systemPipeR: NGS workflow and report generation environment

Accessories function to modify the Command-line Version 1

Description

Accessories function to modify the Command-line Version 1

Usage

printParam(sysargs, position, index = NULL)
subsetParam(sysargs, position, index = NULL, trim = TRUE, mute = FALSE)
replaceParam(sysargs, position, index = NULL, replace, mute = FALSE)
renameParam(sysargs, position, index = FALSE, rename, mute = FALSE)
appendParam(sysargs, position, index = NULL, append, after, mute = FALSE)

Arguments

sysargs	Object of class SYSargs2. Output from the createParamFiles function.
position	string, one of baseCommand, inputs, outputs to view or apply a modification.
index	numeric or character vector, index to view or change a single item in baseCommand, inputs, outputs.
trim	logical, only keep arguments specified by index. Default is "TRUE".
replace	named list, replace arguments in different positions. Replace list length must be the same as index. Different positions will have different requirements.
rename	character vector, rename items in different positions. rename vector length must be the same as index.
append	named list, same requirements as replace, however it cannot append baseCommand.
after	a subscript, after which the values are to be appended. If NULL will be after the last argument or specify a numeric integer.
mute	logical, print the raw command-line string and output after replacing or rename.

Details

- printParam: prints its arguments defined by position and index.

- subsetParam: returns subsets of command-line, keeping the arguments defined by position and index.

- replaceParam: replaces the values in command-line with indices given in list by those given in values

- renameParam: rename the names of the arguments.

- appendParam: Add arguments to the original command line.

Value

SYSargs2 object

Author(s)

Le Zhang and Daniela Cassol

References

For more details on CWL, please consult the following page: https://www.commonwl.org/

See Also

writeParamFiles createParamFiles loadWorkflow renderWF showClass("SYSargs2")

Examples

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> \
    --verbose
"
cmd <- createParamFiles(command)
cmdlist(cmd)

tgirke/systemPipeR documentation built on Aug. 30, 2022, 10 p.m.