Tool Repository

A Tool is the definition of a containerized application with defined inputs, outputs, and execution environment details including compute resources required, environment variables, command line arguments, and more.

Create a Tool

Tools define the inputs, parameters, and outputs for the analysis. Tools are available for use in graphical CWL pipelines by any project in the account.

1. Select System Settings > Tool Repository > + Create.

2. Configure tool settings in the tool properties tabs. See Tool Properties.

3. Select Save.

Tool Properties

The following sections describe the tool properties that can be configured in each tab.

Refer to the CWL CommandLineTool Specification for further explanation about many of the properties described below. Not all features described in the specification are supported.

Details Tab

Field	Entry
Name	The name of the tool.
Description	Free text description for information purposes.
Icon	The icon for the tool.
Status	The release status of the tool.
Docker image	The registered Docker image for the tool.
Categories	One or more tags to categorize the tool. Select from existing tags or type a new tag name in the field.
Tool version	The version of the tool specified by the end user. Could be any string.
Release version	The version number of the tool.
Version comment	A description of changes in the updated version.
Links	External reference links.
Documentation	The Documentation field provides options for configuring the HTML description for the tool. The description appears in the Tool Repository but is excluded from exported CWL definitions.

Tool Status

The release status of the tool. can be one of "Draft", "Release Candidate", "Released" or "Deprecated". The Building and Build Failed options are set by the application and not during configuration.

Status	Description
Draft	Fully editable draft.
Release Candidate	The tool is ready for release. Editing is locked but the tool can be cloned to create a new version.
Released	The tool is released. Tools in this state cannot be edited. Editing is locked but the tool can be cloned to create a new version.
Deprecated	The tool is no longer intended for use in pipelines. but there are no restrictions placed on the tool. That is, it can still be added to new pipelines and will continue to work in existing pipelines. It is merely an indication to the user that the tool should no longer be used.

General Tab

The General provides options to configure the basic command line.

Field	Entry
ID	CWL identifier field
CWL version	The CWL version in use. This field cannot be changed.
Base command	Components of the command. Each argument must be added in a separate line.
Standard out	The name of the file that captures Standard Out (STDOUT) stream information.
Standard error	The name of the file that captures Standard Error (STDERR) stream information.
Requirements	The requirements for triggering an error message. (see below)
Hints	The requirements for triggering a warning message. (see below)

The Hints/Requirements include CWL features to indicate capabilities expected in the Tool's execution environment.

• Inline Javascript

  • The Tool contains a property with a JavaScript expression to resolve it's value.

• Initial workdir

  • The workdir can be any of the following types:

    • String or Expression — A string or JavaScript expression, eg, $(inputs.InputFASTA)

    • File or Dir — A map of one or more files or directories, in the following format: {type: array, items: [File, Directory]}

    • Dirent — A script in the working directory. The Entry name field specifies the file name.

• Scatter feature — Indicates that the workflow platform must support the scatter and scatterMethod fields.

Arguments Tab

The Arguments tab provides options to configure base command parameters that do not require user input.

Tool arguments may be one of two types:

• String or Expression — A literal string or JavaScript expression, eg --format=bam.

• Binding — An argument constructed from the binding of an input parameter.

The following table describes the argument input fields.

Field	Entry	Type
Value	The literal string to be added to the base command.	String or expression
Position	The position of the argument in the final command line. If the position is not specified, the default value is set to 0 and the arguments appear in the order they were added.	Binding
Prefix	The string prefix.	Binding
Item separator	The separator that is used between array values.	Binding
Value from	The source string or JavaScript expression.	Binding
Separate	The setting to require the Prefix and Value from fields to be added as separate or combined arguments. Tru indicates the fields must be added as separate arguments. False indicates the fields must be added as a single concatenated argument.	Binding
Shell quote	The setting to quote the Value from field on the command line. True indicates the value field appears in the command line. False indicates the value field is entered manually.	Binding

Example

Field	Value
Prefix	--output-filename
Value from	$(inputs.inputSAM.nameroot).bam
Input file	/tmp/storage/SRR45678_sorted.sam
Output file	SRR45678_sorted.bam

Inputs Tab

The Inputs tab provides options to define the input files and folders for the tool. The following table describes the input and binding fields. Selecting multi value enables type binding options for adding prefixes to the input.

Field	Entry
ID	The file ID.
Label	A short description of the input.
Description	A long description of the input.
Type	The input type, which can be either a file or a directory.
Input options	Optional indicates the input is optional. Multi value indicates there is more than one input file or directory. Streamable indicates the file is read or written sequentially without seeking.
Secondary files	The required secondary files or directories.
Format	The input file format.
Position	The position of the argument in the final command line. If the position is not specified, the default value is set to 0 and the arguments appear in the order they were added.
Prefix	The string prefix.
Item separator	The separator that is used between array values.
Value from	The source string or JavaScript expression.
Load contents	The setting to require the Prefix and Value from fields to be added as separate or combined arguments. True indicates the fields must be added as separate arguments. False indicates the fields must be added as a single concatenated argument.
Separate	The setting to require the Prefix and Value from fields to be added as separate or combined arguments. True indicates the fields must be added as separate arguments. False indicates the fields must be added as a single concatenated argument.
Shell quote	The setting to quote the Value from field on the command line. True indicates the value field appears in the command line. False indicates the value field is entered manually.

Settings Tab

The Settings tab provides options to define parameters that can be set at the time of execution. The following table describes the input and binding fields. Selecting multi value enables type binding options for adding prefixes to the input.

Field	Entry
ID	The file ID.
Label	A short description of the input.
Description	A long description of the input.
Type	The input type, which can be Boolean, Int, Long, Float, Double or String.
Default Value	The default value to use if the tool setting is not available.
Input options	Optional indicates the input is optional. Multi value indicates there can be more than one value for the input.
Position	The position of the argument in the final command line. If the position is not specified, the default value is set to 0 and the arguments appear in the order they were added.
Prefix	The string prefix.
Item separator	The separator that is used between array values.
Value from	The source string or JavaScript expression.
Separate	The setting to require the Prefix and Value from fields to be added as separate or combined arguments. True indicates the fields must be added as separate arguments. False indicates the fields must be added as a single concatenated argument.
Shell quote	The setting to quote the Value from field on the command line. True indicates the value field appears in the command line. False indicates the value field is entered manually.

Outputs Tab

The Outputs tab provides options to define the parameters of output files.

The following table describes the input and binding fields. Selecting multi value enables type binding options for adding prefixes to the input.

Field	Entry
ID	The file ID.
Label	A short description of the input.
Description	A long description of the input.
Type	The input type, which can be either a file or a directory.
Output options	Optional indicates the input is optional. Multi value indicates here is more than one input file or directory. Streamable indicates the file is read or written sequentially without seeking.
Secondary files	The required secondary files or folders.
Format	The input file format.
Globs	The pattern for searching file names.
Load contents	Automatically loads some contents. The system extracts up to the first 64 KiB of text from the file. Populates the contents field with the first 64 KiB of text from the file.
Output eval	Evaluate an expression to generate the output value.

Edit a Tool

1. From the System Settings > Tool Repository page, select a tool.

2. Select Edit.

Update Tool Status

1. From the System Settings > Tool Repository page, select a tool.

2. Select the Information tab.

3. From the Status drop-down menu, select a status.

4. Select Save.

Creating definitions without the wizard

In addition to the interactive Tool builder, the platform GUI also supports working directly with the raw definition on the right hand side of the screen when developing a new Tool. This provides the ability to write the Tool definition manually or bring an existing Tool's definition to the platform.

Be careful when editing the raw tool definition as this can introduce errors.

A simple example CWL Tool definition is provided below.

#!/usr/bin/env cwl-runner

cwlVersion: v1.0
class: CommandLineTool
label: echo
inputs:
  message:
    type: string
    default: testMessage
    inputBinding:
      position: 1
outputs:
  echoout:
    type: stdout
baseCommand:
- echo

After pasting into the editor, the definition is parsed and the other tabs for visually editing the Tool will populate according to the definition contents.

Creating Your First Tool - Tips and Tricks

• General Tool - includes your base command and various optional configurations.

  • The base command is required for your tool to run, e.g. python /path/to/script.py such that python and /path/to/script.py are added in separate lines.

  • Inline Javascript requirement - must be enabled if you are using Javascript anywhere in your tool definition.

  • Initial workdir requirement - Dirent Type

    • Your tool must point to a script that executes your analysis. That script can either be provided in your Docker image or using a Dirent. Defining a script via Dirent allows you to dynamically modify your script without updating your Docker image. In order to define your Dirent script define your script name under Entry name (e.g. runner.sh) and the script content under Entry. Then, point your base command to that custom script, e.g. bash runner.sh.

The difference between Settings and Arguments: Settings are exposed at the pipeline level with the ability to get modified at launch, while Arguments are intended to be immutable and hidden from users launching the pipeline.

• How to reference your tool inputs and settings throughout the tool definition?

  • You can either reference your inputs using their position or ID.

    • Settings can be referenced using their defined IDs, e.g. $(inputs.InputSetting)

    • File/Folder inputs can be referenced using their defined IDs, followed by the desired field, e.g. $(inputs.InputFile.path). For additional information please refer to the File CWL documentation.

    • All inputs can also be referenced using their position, e.g. bash script.sh $1 $2