ParamFiles.Rd
Accessories function to modify the Command-line Version 1
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)
Object of class SYSargs2
. Output from the createParamFiles
function.
string, one of baseCommand
, inputs
, outputs
to view or apply a modification.
numeric or character vector, index to view or change a single item in
baseCommand
, inputs
, outputs
.
logical, only keep arguments specified by index
. Default is "TRUE".
named list, replace arguments in different positions. Replace list length
must be the same as index
. Different positions will have different requirements.
character vector, rename items in different positions. rename
vector length
must be the same as index
.
named list, same requirements as replace
, however it cannot append baseCommand
.
a subscript, after which the values are to be appended. If NULL
will be
after the last argument or specify a numeric integer.
logical, print the raw command-line string and output after replacing or rename.
- 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.
SYSargs2
object
For more details on CWL
, please consult the following page: https://www.commonwl.org/
writeParamFiles
createParamFiles
loadWorkflow
renderWF
showClass("SYSargs2")
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)
#> *****BaseCommand*****
#> hisat2
#> *****Inputs*****
#> S:
#> type: File
#> preF: -S
#> yml: ./results/M1A.sam
#> x:
#> type: File
#> preF: -x
#> yml: ./data/tair10.fasta
#> k:
#> type: int
#> preF: -k
#> yml: 1
#> min-intronlen:
#> type: int
#> preF: -min-intronlen
#> yml: 30
#> max-intronlen:
#> type: int
#> preF: -max-intronlen
#> yml: 3000
#> threads:
#> type: int
#> preF: -threads
#> yml: 4
#> U:
#> type: File
#> preF: -U
#> yml: ./data/SRR446027_1.fastq.gz
#> verbose:
#> type:
#> preF: --verbose
#> yml:
#> *****Outputs*****
#> output1:
#> type: File
#> value: ./results/M1A.sam
#> *****Parsed raw command line*****
#> hisat2 -S ./results/M1A.sam -x ./data/tair10.fasta -k 1 -min-intronlen 30 -max-intronlen 3000 -threads 4 -U ./data/SRR446027_1.fastq.gz --verbose
#> Written content of 'commandLine' to file:
#> param/cwl/hisat2/hisat2.cwl
#> Written content of 'commandLine' to file:
#> param/cwl/hisat2/hisat2.yml
cmdlist(cmd)
#> $defaultid
#> $defaultid$hisat2
#> [1] "hisat2 -S ./results/M1A.sam -x ./data/tair10.fasta -k 1 -min-intronlen 30 -max-intronlen 3000 -threads 4 -U ./data/SRR446027_1.fastq.gz --verbose "
#>
#>