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StandardProcess

Executes a given system command. The given input is delivered to the standard input stream and the output streams are bind to the output ports. Input files and folders can be used as command like arguments by binding them to the optional argument inputs of this component and by including the corresponding tags to the command statement.

The executable may produce some output files in addition to its standard output. You can bind these outputs to the optional output ports by assigning their names to the command.

Version 1.3
Bundle builtin
Categories
Specialties generic
Authors Marko Laakso (Marko.Laakso@Helsinki.FI)
Issue tracker View/Report issues
Requires microarray.jar (jar)
Source files component.xml
Usage Example with default values

Type parameters (generics)

Inputs

Name Type Mandatory Description
input BinaryFile Optional Standard input stream for the executable
env Properties Optional A set of environment variables
arg1 A1 (generic) Optional An input argument referred as @arg1@ in command
arg2 A2 (generic) Optional An input argument referred as @arg2@ in command
arg3 A3 (generic) Optional An input argument referred as @arg3@ in command
arg4 A4 (generic) Optional An input argument referred as @arg4@ in command
arg5 A5 (generic) Optional An input argument referred as @arg5@ in command
arg6 A6 (generic) Optional An input argument referred as @arg6@ in command
arg7 A7 (generic) Optional An input argument referred as @arg7@ in command
arg8 A8 (generic) Optional An input argument referred as @arg8@ in command
arg9 A9 (generic) Optional An input argument referred as @arg9@ in command

Outputs

Name Type Description
stdout BinaryFile Standard output of the executable
stderr BinaryFile Standard error of the executable
optOut1 O1 (generic) An optional output file referred as @optOut1@ in command
optOut2 O2 (generic) An optional output file referred as @optOut2@ in command
optOut3 O3 (generic) An optional output file referred as @optOut3@ in command

Parameters

Name Type Default Description
command string (no default) Command to be launched
delim string "" Delimiter of the command arguments. An empty string can be used for white spaces.
wd string "" Working directory for the executable if not the component folder

Test cases

Test case Parameters IN
input
IN
env
IN
arg1
IN
arg2
IN
arg3
IN
arg4
IN
arg5
IN
arg6
IN
arg7
IN
arg8
IN
arg9
OUT
stdout
OUT
stderr
OUT
optOut1
OUT
optOut2
OUT
optOut3
case1 properties input (missing) (missing) (missing) (missing) (missing) (missing) (missing) (missing) (missing) (missing) stdout stderr optOut1 optOut2 optOut3

command=head -2

case2 properties (missing) env (missing) (missing) (missing) (missing) (missing) (missing) (missing) (missing) (missing) stdout stderr (missing) (missing) (missing)

command=env

case3 properties (missing) (missing) (missing) arg2 arg3 (missing) (missing) (missing) (missing) (missing) (missing) stdout stderr (missing) (missing) (missing)

command = cat @arg2@ @arg3@ @arg2@

case4 properties (missing) (missing) (missing) (missing) (missing) arg4 (missing) (missing) (missing) (missing) (missing) (expecting failure) (expecting failure) (expecting failure) (expecting failure) (expecting failure)

command = date

case5 properties (missing) (missing) (missing) (missing) (missing) (missing) (missing) (missing) (missing) (missing) (missing) (expecting failure) (expecting failure) (expecting failure) (expecting failure) (expecting failure)

command = cat @arg1@

case6 properties input (missing) (missing) (missing) (missing) (missing) (missing) (missing) (missing) (missing) (missing) stdout stderr optOut1 optOut2 optOut3

command = tee @optOut1@

case7 properties input (missing) (missing) (missing) (missing) (missing) (missing) (missing) (missing) (missing) (missing) stdout (missing) (missing) (missing) (missing)

command = grep\n[A-Z]\t[A-Z],
delim = \n


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