printParam {systemPipeR} | R Documentation

## Accessories function to modify the Command-line

### Description

Accessories function to modify the Command-line

### 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)

[Package systemPipeR version 2.0.8 Index]