printParam | R Documentation |
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)
sysargs |
Object of class |
position |
string, one of |
index |
numeric or character vector, index to view or change a single item in
|
trim |
logical, only keep arguments specified by |
replace |
named list, replace arguments in different positions. Replace list length
must be the same as |
rename |
character vector, rename items in different positions. |
append |
named list, same requirements as |
after |
a subscript, after which the values are to be appended. If |
mute |
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
Le Zhang and Daniela Cassol
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) cmdlist(cmd)
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