Create toolapp

Stdout redirect: If you want to save the standard output from the tool, enter the name of the file you want to use here. The filename can include a dynamic expression.

Create toolholder

Stdin redirect: If you want to pipe data into standard input when the tool runs, enter the name of the file containing the data here. The filename can include a dynamic expression.

Arguments are command options and parameters that you want to set to predefined values that are applied every time when the tool executes. Arguments can also include dynamic expressions. For example, you could use a fixed expression that generates the output file name based on the name of an input file.

Create toolreview

Create toolqctp

If the argument could be positioned immediately after the base command in the command line, you could set it as part of the base command instead. But note that CWL v1.x versions do not support dynamic expressions in base commands, so if you need a dynamic expression you will have to use an argument.

For CWL 1.0 tools, the Output Eval field will be populated with the expression that will be used for inheriting metadata. If there is a conflict, you will see a warning under the ID field and will be able to solve the issue by editing the expression in the Output Eval field.

Note: If you are using CWL v1.x, you cannot include expressions in the base command, so any dynamic expressions need to be specified as an argument, not as part of the base command.

The base command is the part of the command before any items you want to specify as inputs to be resolved at runtime. This will include the command itself, and usually the sub-command, if present. It may also include command options and parameters that you want to set to hard-coded values, provided these can be positioned at the start of the command line. Alternatively, hardcoded command options and parameters can be defined as arguments, which can have defined positions in the command line.

If you are using the Seven Bridges Platform on AWS EU, please use eu-images.sbgenomics.com as the image registry instead of images.sbgenomics.com.

Create toolMultifix

Description Contains text fields that help describe the functionality of the output port in more detail. For specific information about each of the fields, please see Description in the Input ports section above.

Create toolqctp toolpost

If the image is in the Seven Bridges image registry, the format is images.sbgenomics.com//[:tag], where:

These are any additional files the tool needs to run that aren’t already included in the Docker container. For example, you could specify a configuration file here instead of installing it in the Docker container. Any files specified here will be created in the working directory when the tool executes.

Computational resources specify the minimum resource requirements for the tool. The execution will fail if the resources specified here cannot be allocated.

You can specify everything in the base command as a single section, or, if you are using the sbg:draft-2 version of CWL, you can build this up in multiple sections. If you want to include dynamic expressions in the base command (CWL sbg:draft-2 only), you will have to use separate sections for each fixed part and each dynamic expression as you can’t mix fixed items and dynamic items in the same section.

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For apps described using the sbg:draft-2 version of CWL you can switch back to the legacy editor by clicking your username in the top-right corner of the editor and selecting Switch back to the legacy editor.

The following properties can be set in the object inspector for an output port. For more information, see the details on output ports.