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Up: Component summary
Component
StandardProcessExecutes 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 |
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 |
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| case2 | properties | (missing) | env | (missing) | (missing) | (missing) | (missing) | (missing) | (missing) | (missing) | (missing) | (missing) | stdout | stderr | (missing) | (missing) | (missing) |
|
command=env |
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| case3 | properties | (missing) | (missing) | (missing) | arg2 | arg3 | (missing) | (missing) | (missing) | (missing) | (missing) | (missing) | stdout | stderr | (missing) | (missing) | (missing) |
|
command = cat @arg2@ @arg3@ @arg2@ |
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| 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 |
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| 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@ |
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| case6 | properties | input | (missing) | (missing) | (missing) | (missing) | (missing) | (missing) | (missing) | (missing) | (missing) | (missing) | stdout | stderr | optOut1 | optOut2 | optOut3 |
|
command = tee @optOut1@ |
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| 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], |
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