ParamFiles2.Rd
Accessories function to modify the Command-line Version 2
printParam2(sysargs, base = FALSE, args = FALSE, inputs = FALSE,
outputs = FALSE, stdout = FALSE, raw_cmd = FALSE, all = TRUE)
appendParam2(sysargs, x, position = c("inputs", "args", "outputs"),
after = NULL, verbose = FALSE)
replaceParam2(sysargs, x, index=NULL,
position = c("inputs", "baseCommand", "args", "outputs", "stdout"),
verbose = FALSE)
removeParam2(sysargs, index=NULL, position = c("inputs", "args", "outputs", "stdout"),
verbose = FALSE)
renameParam2(sysargs, index=NULL, new_names,
position = c("inputs", "args", "outputs", "stdout"), verbose = FALSE)
Object of class SYSargs2
. Output from the createParamFiles
function.
logical, print out base command information?
logical, print out arguments information?
logical, print out inputs information?
logical, print out outputs information?
logical, print out stdout information?
logical, print out parsed raw command information?
logical, print out all base command, arguments, inputs,
outputs, and raw command information?
Turn this to TRUE
will overwrite all above to TRUE
.
If you need to print out selected positions, turn this to FALSE
and turn
other positions to TRUE
.
string, one of the positions to apply a modification.
For appendParam2
: "inputs", "args", "outputs",
for replaceParam2
: "inputs", "baseCommand", "args", "outputs", "stdout",
for removeParam2
, renameParam2
: "inputs", "args", "outputs", "stdout".
numeric or character vector, index of items to remove or rename item(s)
inside the position you choose, in removeParam2
, renameParam2
,
replaceParam2
.
integer, in appendParam2
, after which current item you want to append
the new items in the position you have selected? For example, if you want
the new item to be the first, then use 0
, if last, then use
999
to make sure it goes to the last one.
named list or string, new items to replace or append in different positions. Replace list length
must be the same as index
. Different positions will have different requirements.
See details of the x
format requirements.
character vector, new names that you wish to replace the old names. new_names
vector length
must be the same as index
in renameParam2
.
logical, show addtional information during/after operation? for example, print the new changes.
- printParam2
: prints its arguments defined by position
and index
.
- removeParam2
: removes items in certain positions you select.
- replaceParam2
: replaces the values in command-line with indices given in list by those given in values
- renameParam2
: rename the names of items in certain position.
- appendParam2
: Add arguments to the original command line. Adding new basecommand or
standard out is not allowed.
- If x
is a character, it requires exact 3 semi-colons ;
to separate the string
in to 4 columns. Values before the third column is the same as createParam
inputs,
first column: prefix/argument name, second column: type, third column: default value.
The fourth column (new): numeric, index of the new item, this will be translated into
position
entries in CWL.
- If x
is a list, it must be named. Following items must be included in list:
preF
, type
, value
, index
. They refer to prefix, param type,
default value, and position index correspondingly.
SYSargs2
object
For more details on CWL
, please consult the following page: https://www.commonwl.org/
writeParamFiles
createParamFiles
loadWorkflow
renderWF
showClass("SYSargs2")
command2 <- '
mycmd2 \
p: -s; File; sample1.txt \
p: -s; File; sample2.txt \
p: --c; ; \
p: -o; File; out: myout.txt \
ref_genome; File; a.fasta \
p: --nn; int; 12 \
mystdout; File; stdout: abc.txt
'
cmd2 <- createParam(command2, syntaxVersion = "v2", writeParamFiles=FALSE)
#> *****BaseCommand*****
#> mycmd2
#> *****Arguments*****
#> argument1:
#> prefix: --c
#> position: 3
#> *****Inputs*****
#> s1:
#> type: File
#> prefix: -s
#> default value: sample1.txt
#> position: 1
#> s2:
#> type: File
#> prefix: -s
#> default value: sample2.txt
#> position: 2
#> o:
#> type: File
#> prefix: -o
#> default value: myout.txt
#> position: 4
#> ref_genome:
#> type: File
#> prefix:
#> default value: a.fasta
#> position: 5
#> nn:
#> type: int
#> prefix: --nn
#> default value: 12
#> position: 6
#> *****Outputs*****
#> output1:
#> type: File
#> default value: myout.txt
#> *****Standard Outputs*****
#> mystdout:
#> type: File
#> default value: abc.txt
#> *****Parsed raw command line*****
#> mycmd2 -s sample1.txt -s sample2.txt --c -o myout.txt a.fasta --nn 12 > abc.txt
# string format
new_cmd <- 'p: -abc; string; abc; 7'
cmd2 <- appendParam2(cmd2, x = new_cmd, position = "inputs")
printParam2(cmd2, all = FALSE, inputs = TRUE, raw_cmd = TRUE)
#> *****Inputs*****
#> s1:
#> type: File
#> prefix: -s
#> default value: sample1.txt
#> position: 1
#> s2:
#> type: File
#> prefix: -s
#> default value: sample2.txt
#> position: 2
#> o:
#> type: File
#> prefix: -o
#> default value: myout.txt
#> position: 4
#> ref_genome:
#> type: File
#> prefix:
#> default value: a.fasta
#> position: 5
#> nn:
#> type: int
#> prefix: --nn
#> default value: 12
#> position: 6
#> abc:
#> type: string
#> prefix: -abc
#> default value: abc
#> position: 7
#> *****Parsed raw command line*****
#> mycmd2 -s sample1.txt -s sample2.txt --c -o myout.txt a.fasta --nn 12 -abc abc > abc.txt
# list format
new_cmd <- list(name = "new_arg", preF = "--foo", index = "8")
cmd2 <- appendParam2(cmd2, x = new_cmd, position = "args")
printParam2(cmd2, all = FALSE, args = TRUE, raw_cmd = TRUE)
#> *****Arguments*****
#> argument1:
#> prefix: --c
#> position: 3
#> new_arg:
#> prefix: --foo
#> position: 8
#> *****Parsed raw command line*****
#> mycmd2 -s sample1.txt -s sample2.txt --c -o myout.txt a.fasta --nn 12 -abc abc --foo > abc.txt
# rename
cmd2 <- renameParam2(cmd2, "new_name_arg", index = "new_arg", position = "args")
printParam2(cmd2, all = FALSE, args = TRUE, raw_cmd = TRUE)
#> *****Arguments*****
#> argument1:
#> prefix: --c
#> position: 3
#> new_name_arg:
#> prefix: --foo
#> position: 8
#> *****Parsed raw command line*****
#> mycmd2 -s sample1.txt -s sample2.txt --c -o myout.txt a.fasta --nn 12 -abc abc --foo > abc.txt
# remove
cmd2 <- removeParam2(cmd2, index = "new_name_arg", position = "args")
printParam2(cmd2, all = FALSE, args = TRUE, raw_cmd = TRUE)
#> *****Arguments*****
#> argument1:
#> prefix: --c
#> position: 3
#> *****Parsed raw command line*****
#> mycmd2 -s sample1.txt -s sample2.txt --c -o myout.txt a.fasta --nn 12 -abc abc > abc.txt