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.
Select System Settings > Tool Repository > + New tool.
Configure tool settings in the tool properties tabs. See Tool Properties.
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.
Information Tab
Field | Entry |
---|---|
Name | The name of the tool. |
Categories | One or more tags to categorize the tool. Select from existing tags or type a new tag name in the field. |
Icon | The icon for the tool. |
Description | Free text description for information purposes. |
Status | The release status of the tool. |
Docker image | The registered Docker image for the tool. |
Regions | The regions supported by linked Docker image. |
Tool version | The version of the tool specified by the end user. Could be any string. |
Release version | The version number of the tool. |
Family | A group of tools or tool versions. |
Version comment | A description of changes in the updated version. |
Links | External reference links. |
Tool Status
The release status of the tool. can be one of "Draft", "Release Candidate", "Released" or "Deprecated".
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. |
Documentation Tab
The Documentation tab provides options for configuring the HTML description for the tool. The description appears in the Tool Repository but is excluded from exported CWL definitions.
General Tool Tab
The General Tool tab 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. |
Interpreter version | The interpreter version in use. |
Base command | Components of the command. Each argument must be added in a separate line. |
Standard in | The name of the file that captures Standard In (STDIN) stream information. |
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. |
Hints | The requirements for triggering a warning message. |
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
andscatterMethod
fields.
Tool Arguments Tab
The Tool 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 |
|
Value from |
|
Input file |
|
Output file |
|
Tool Input Tab
The Tool Inputs tab provides options to define the input files and directories 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 | Checkboxes to add the following 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. |
Tool Settings Tab
The Tool 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. |
Default Value | The default value to use if the tool setting is not available. |
Type | The input type, which can be Boolean, Int, Long, Float, Double or String. |
Input options | Checkboxes to add the following 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. |
Tool Outputs Tab
The Tool 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. |
Default Value | A long description of the input. |
Type | The input type, which can be either a file or a directory. |
Output options | Checkboxes to add the following 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 directories. |
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. |
Tool CWL Tab
The Tool CWL tab displays the complete CWL code constructed from the values entered in the other tabs. the CWL code automatically updates when changes are made in the tool definition tabs, and any changes to the CWL code are reflected in the tool definition tabs.
❗️ Modifying data within the CWL editor can result in invalid code.
Edit a Tool
From the System Settings > Tool Repository page, select a tool.
Select Edit.
Update Tool Status
From the System Settings > Tool Repository page, select a tool.
Select the Information tab.
From the Status drop-down menu, select a status.
Select Save.
Import Tool
In addition to the interactive Tool builder, the platform GUI also supports working directly with the raw definition 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.
A simple example CWL Tool definition is provided below.
When creating a new Tool, navigate to System Settings > Tool Repository > your_tool > Tool CWL tab to show the raw CWL definition. Here a CWL CommandLineTool definition may be pasted into the editor. 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 thatpython
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 underEntry
. Then, point your base command to that custom script, e.g.bash runner.sh
.
❗ What's 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/Directory 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
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