createParamFiles: createParamFiles

Description Usage Arguments Details Value Author(s) References See Also Examples

View source: R/cmdToCWL.R

Description

The constructor function creates an SYSargs2 S4 class object from command-line string. Also, the function creates and saves the CWL param files. The latest storages all the parameters required for running command-line software, following the standard and specification defined on Common Workflow Language (CWL).

Usage

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createParamFiles(commandline, cwlVersion = "v1.1", class = "CommandLineTool",
                  results_path = "./results", module_load = "baseCommand", 
                  file = "default", writeParamFiles = FALSE, overwrite = FALSE, 
                  silent = FALSE)
                  
writeParamFiles(sysargs, file = "default", overwrite = TRUE, silent = FALSE)

Arguments

commandline

string. Original command-line to create the CWL files from. Please see Details for more information.

cwlVersion

string. The version of the Common Workflow Language. More information here: https://www.commonwl.org/.

class

character. Name of Common Workflow Language Description class. The following is accepted: CommandLineTool.

results_path

Path to the results folder. Default is results.

module_load

string, Name of software to load by Environment Modules system. Default is "baseCommand", which creates a subfolder and two files: *.cwl and *.yml at ./param/cwl/.

file

character. Name and path of output files. If set to "default" then the name of the output files will have the pattern <software>.cwl and <software>.yml, where <software> will be what baseCommand(x) returns, when x is an object of class SYSargs2. Also, it creates a subfolder at ./param/cwl/ with name <software>.

writeParamFiles

logical. If set to TRUE, it will write to file the content of the CWL files:*.cwl and *.yml. Default is FALSE.

overwrite

logical. If set to TRUE, existing files of the same name will be overwritten. Default is FALSE.

silent

logical. If set to TRUE, all messages returned by the function will be suppressed. Default is FALSE.

sysargs

Object of class SYSargs2. Output from the createParamFiles function.

Details

- First line of the command-line object will be treated as the baseCommand;

- For argument lines (starting from the second line), any word before the first space with leading '-' or '–' in each will be treated as a prefix, like -S or --min. Any line without this first word will be treated as no prefix;

- All defaults are placed inside <...>;

- First argument is the input argument type. F for "File", int for integer, string for string;

- Optional: use the keyword out followed the type with a , comma separation to indicate if this argument is also a CWL output;

- Then, use : to separate keywords and default values, any non-space value after the : will be treated as the default value;

- If any argument has no default value, just a flag, like --verbose, there no need to add any <...>.

- The \ is not required, however for consistency it is recommended to add.

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 printParam subsetParam replaceParam renameParam appendParam loadWorkflow renderWF showClass("SYSargs2")

Examples

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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 July 20, 2021, 10:45 p.m.