Handling of exclusive/dependent inputs

More guidance on how to use dependent and mutually exclusive inputs in a multi-stepped workflow would be nice.
I could only find something in the FAQ: [https://www.commonwl.org/user_guide/faq.html#contents](https://www.commonwl.org/user_guide/faq.html#contents)

Some examples for dependent workflows. _Credit goes to @alexiswl_

**command line too cwl:**
```
cwlVersion: v1.2
class: CommandLineTool
inputs:
dependent_parameters:
type:
type: record
name: dependent_parameters
fields:
itemA:
type: string
inputBinding:
prefix: -A
itemB:
type: string
inputBinding:
prefix: -B
outputs:
example_out:
type: stdout
stdout: output.txt
baseCommand: echo
```
If the workflow input type is the same record schema as the tool, you can simply parse them like you do with any object such as a file or directory.
**record_wf.cwl**
```
cwlVersion: v1.2
class: Workflow

inputs:
dependent_parameters:
type:
type: record
name: dependent_parameters
fields:
itemA:
type: string
itemB:
type: string

steps:
record:
run: record.cwl
in:
dependent_parameters: dependent_parameters
out: [example_out]

outputs:
example_out:
type: File
outputSource: record/example_out
```

Things get a little tricky when you need to convert a record type from the directory to the workflow
i.e let's say your workflow has itemC instead of itemB, but your tool has the existing itemA / itemB record type.

One way to convert is by using the valueFrom attribute in the step input (note the requirements update needed to the workflow)
**record_wf.cwl**
```
#!/usr/bin/env cwl-runner
cwlVersion: v1.2
class: Workflow

# Requirements needed for workflow
# valueFrom requires StepInputExpressionRequirement
# While any javascript code present will require the InlineJavascriptRequirement
requirements:
StepInputExpressionRequirement: {}
InlineJavascriptRequirement: {}

inputs:
dependent_parameters:
type:
type: record
name: dependent_parameters
fields:
itemA:
type: string
itemC: # New record type
type: string

steps:
record:
run: record.cwl # Expects old record type
in:
dependent_parameters:
source: dependent_parameters
valueFrom: |
${
return {
"itemA": self.itemA,
"itemB": self.itemC
}
}
out: [example_out]

outputs:
example_out:
type: File
outputSource: record/example_out
```
Let's test this with our input yaml
```
dependent_parameters:
itemA: a_string # type "string
itemC: c_string # type "string"
```
```
cwltool record-wf.cwl input.yaml
```
Gives
```
INFO /usr/bin/cwltool 3.1.20220224085855
INFO Resolved 'record-wf.cwl' to 'file:///tmp/tmp.gkj56GiQ0w/record-wf.cwl'
INFO [workflow ] start
INFO [workflow ] starting step record
INFO [step record] start
INFO [job record] /tmp/oq_5u9f8$ echo \
-A \
a_string \
-B \
c_string > /tmp/oq_5u9f8/output.txt
INFO [job record] completed success
INFO [step record] completed success
INFO [workflow ] completed success
{
"example_out": {
"location": "file:///tmp/tmp.gkj56GiQ0w/output.txt",
"basename": "output.txt",
"class": "File",
"checksum": "sha1$f215e8565d4711ed1fac71938dee09ef7781870f",
"size": 24,
"path": "/tmp/tmp.gkj56GiQ0w/output.txt"
}
}
INFO Final process status is success
```
**output.txt**
```
-A a_string -B c_string
```
Let's instead assume an eggnog-mapper tool requires the inputs input_fasta, data_dir, db and diamond_db, we can instead use the JavaScript expression / valueFrom syntax shown above to collect each of these attributes from the eggnog input record.

For example
```
in:
input_fasta: bakta/sequences_cds
data_dir:
source: eggnog
valueFrom: |
${
return self.data_dir;
}
db:
source: eggnog
valueFrom: |
${
return self.db;
}
diamond_db:
source: eggnog
valueFrom: |
${
return self.diamond_db;
}
```

This last example could be more generalized...