Tool Commands
s4ns tool commands are designed to facilitate the interoperability with CWL CommandLineTools. The tool command itself has three subcommands for basic CR~~U~~D operations: create, list and remove.
Usage
Provides commands to create and work with CWL CommandLineTools
Usage: s4n tool <COMMAND>
Commands:
create Runs commandline string and creates a tool (synonym: s4n run)
list Lists all tools [aliases: ls]
remove Remove a tool, e.g. s4n tool rm toolname [aliases: rm]
help Print this message or the help of the given subcommand(s)
Options:
-h, --help Print help
tool create
The tool create command can be used to easily generate CWL CommandLineTools. It serves as a prefix to the usual command line prompt. Calling tool create with a command attached will execute the command, determine in- and outputs and create a CWL tool definition file in the workflows folder. s4n tool create has s4n run as alias for even less typing.
Note
Before using this command all changes need to be commited as it uses git to determine tool outputs!
git status can be used to check beforehand.
Tip
Redirection > and pipes | can be used, but need to be escaped with a backslash fot the parser to use. Otherwise the console output of s4n will be redirected / piped.
Usage
Runs commandline string and creates a tool (synonym: s4n run)
Usage: s4n tool create [OPTIONS] [COMMAND]...
Arguments:
[COMMAND]... Command line call e.g. python script.py [ARGUMENTS]
Options:
-n, --name <NAME> A name to be used for this tool
-c, --container-image <CONTAINER_IMAGE> An image to pull from e.g. docker hub or path to a Dockerfile
-t, --container-tag <CONTAINER_TAG> The tag for the container when using a Dockerfile
-r, --raw Outputs the raw CWL contents to terminal
--no-commit Do not commit at the end of tool creation
--no-run Do not run given command
--clean Deletes created outputs after usage
-h, --help Print help
Example
The following command will create a CWL CommandLineTool description for executing a python script echo.py with a txt file as parameter --test.
#!/usr/bin/env cwl-runner
cwlVersion: v1.2
class: CommandLineTool
requirements:
- class: InitialWorkDirRequirement
listing:
- entryname: echo.py
entry:
$include: '../../echo.py'
inputs:
- id: test
type: File
default:
class: File
location: '../../input.txt'
inputBinding:
prefix: '--test'
outputs:
- id: results
type: File
outputBinding:
glob: results.txt
baseCommand:
- python
- echo.py
Options
With the --name option the resulting filename can be manipulated. Without the argument SciWIn client will automatically generate a name based on the command. If for example the same base command is used in two tools there would be a file name conflict.
The two container options --container-image and --container-tag can be used to add Docker requirements to the resulting CWL file. However Docker will NOT be used to execute the script while generating the tool, so make sure to either use s4n in Docker container or provide all neccesary tools for it to run.
With the --raw flag no CWL file will be written to disk. Instead the raw cwl will be outputted to the command prompt (stdout) to process it further.
As tool create needs all changes to be commited beforehand it will create a commit after it completed the tool creation. To prevent that because e.g. manual changes to the CWL file have to be made before committing the --no-commit flag can be used.
Some scripts tend to run for a very long time - e.g. quantum chemistry calculations. To prevent the tool from running the --no-run flag can be used. If this flag is set the parser will just use information from the command line to create the tool, outputs need to be set manually.
TODO: Manual In and Outputs!!! (See #44)
Sometimes it can be beneficial to not commit the created outputs. With the --clean flag all outputs will be deleted before commiting the freshly created tool.
tool list
tool list or tool ls can be used to list all existing tools. Using the command without the -a flag just ouputs the names of all existing tools in the project. Using the -all (or -a) flag will also output the tools in- and outputs which than can easily be used for the workflow connect command.
Usage
tool remove
The tool remove or tool rm command can be used to delete one or more CWL CommandLineTools.