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Updated titles to use consistent capitalization (#330)
Co-authored-by: Peter Amstutz <[email protected]>
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CONTRIBUTING.md

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Use “tool description” not “tool wrapper” for describing the first argument
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given to the `cwl-runner` or `cwltool` commands.
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### Code examples
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### Code Examples
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To include code into a Markdown file you have two options. For external files use
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the following command:

src/faq.md

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:backlinks: "top"
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```
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## Non "`File`" types using `evalFrom`
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## Non "`File`" Types Using `evalFrom`
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```yaml
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cwlVersion: v1.0 # or v1.1
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outputEval: $(self[0].contents)
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```
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## Rename an input file
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## Rename an Input File
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This example demonstrates how to change the name of an input file
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as part of a tool description.
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entryName: $(inputs.src1.basename)_custom_extension
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```
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## Rename an output file
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## Rename an Output File
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This example demonstrates how to change the name of an output file
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from the default name given to it by a tool:
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outputEval: ${self[0].basename=inputs.otu_table_name; return self;}
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```
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## Referencing a local script
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## Referencing a Local Script
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There are two ways to reference a local script:
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In CWL, everything must be directly stated.
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```
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## Setting `self`-based input bindings for optional inputs
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## Setting `self`-based Input Bindings for Optional Inputs
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Currently, `cwltool` can't cope with missing optional inputs if their
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input binding makes use of `self`.
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outputs: []
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```
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## Model a "one-or-the-other" parameter
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## Model a "one-or-the-other" Parameter
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Below is an example showing how
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to specify different strings to be added to a command line,
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outputs: []
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```
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## Connect a solo value to an input that expects an array of that type
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## Connect a Solo Value to an Input that Expects an Array of that Type
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Using [`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/Workflow.html#MultipleInputFeatureRequirement)
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along with
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My String: $(input.stringvalue)
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```
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## `cwltool` errors due to filenames with space characters inside
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## `cwltool` Errors due to Filenames with Space Characters Inside
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`cwltool` does not allow some characters in filenames by default.
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If you can not avoid these dangerous characters, then pass `--relax-path-checks` to `cwltool`.
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## CWL Parameter Reference error due to hyphen in input identifier
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## CWL Parameter Reference Error due to Hyphen in Input Identifier
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If `cwltool --validate` returns valid
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those Docker format containers using the Singularity engine. Directly
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specifying a Singularity format container is not part of the CWL standards.
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## Debug JavaScript expressions
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## Debug JavaScript Expressions
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You can use the <code>--js-console</code> option of <code>cwltool</code>, or you can try
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creating a JavaScript or TypeScript project for your code, and load it

src/introduction/basic-concepts.md

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in more detail. If you are already familiar with CWL or you are looking for more advanced
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content, you may want to skip this section.
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## The CWL specification
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## The CWL Specification
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```{include} /_includes/what-is-cwl.md
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```
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that are required, hints list optional features. Requirements are explained
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in detail in the [Requirements](../topics/requirements-and-hints.md) section.
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## FAIR workflows
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## FAIR Workflows
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> The FAIR principles have laid a foundation for sharing and publishing
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> digital assets, and in particular, data. The FAIR principles emphasize
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`cwltool` also uses the PROV-O standard ontology for data provenance.
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## Learn more
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## Learn More
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- Semantic Versioning - <https://semver.org/>
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- The CWL Specification page in the CWL website: <https://www.commonwl.org/specification/>

src/introduction/prerequisites.md

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Your operating system also needs internet access and a recent version of Python (3.6+).
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```
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## CWL runner
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## CWL Runner
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% https://github.com/common-workflow-language/user_guide/issues/166
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% https://github.com/common-workflow-language/user_guide/issues/64
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:caption: Running `true.cwl` with `cwltool`.
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```
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### cwl-runner Python module
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### Cwl-runner Python Module
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`cwl-runner` is an implementation-agnostic alias for CWL Runners. This simply means that the `cwl-runner` alias command can be invoked independently, and is not reliant on a particular CWL runner.
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Users can invoke `cwl-runner` instead of invoking a CWL runner like `cwltool`
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## Learn more
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## Learn More
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- The [Implementations](basic-concepts.md#implementations) topic in the next section, Basic Concepts.
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- The Python `venv` module: <https://docs.python.org/3/library/venv.html>

src/introduction/quick-start.md

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more about this in the [basic concepts](basic-concepts.md) section.
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```
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## Installing a CWL runner
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## Installing a CWL Runner
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`cwltool` is an implementation of the CWL specification. It is also the
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CWL *Reference Runner* for the specification, and it is compliant with the
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files.
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```
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## Learn more
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## Learn More
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Continue reading the next sections of this User Guide!
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- [List of CWL Implementations](https://www.commonwl.org/implementations).

src/topics/expressions.md

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[file-prop]: https://www.commonwl.org/v1.0/CommandLineTool.html#File
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## Using external libraries and inline JavaScript code with `expressionLib`
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## Using External Libraries and Inline JavaScript Code with `expressionLib`
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The requirement `InlineJavascriptRequirement` supports an `expressionLib` attribute
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that allows users to load external JavaScript files, or to provide inline JavaScript

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