Add user defined YAML tools #19434
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Add user defined YAML tools #19434
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The primary benefit is that the command section does not have access the
app or any dangling reference to the database connection or any other
secrets. There are two flavors here, one uses base_command and
arguments, and allows building up an (escaped) argv list, the other is a
shortcut for writing shell scripts and feels maybe a bit more like
writing a very simple cheetah section.
base_command:
```yml
name: base_command tool
class: GalaxyTool
version: 1.0.0
base_command: cat
arguments:
- $(inputs.input.path)
- '>'
- output.fastq
inputs:
- type: data
name: input
outputs:
output:
type: data
from_work_dir: output.fastq
name: output
```
shell_command style:
```yml
name: shell_command tool
class: GalaxyTool
version: 1.0.0
shell_command: cat '$(inputs.input.path)' > output.fastq
inputs:
- type: data
name: input
outputs:
output:
type: data
from_work_dir: output.fastq
name: output
```
Will probably need this later for efficiency and ignoring `$()` outside of shell_command.
Simply re-use models by index and set values. It's currently a high-water mark situation, and there will be a warning once 200 models (i.e. 200 embedded fragments) are created, but that seems pretty unlikely.
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This work enhances the existing YAML tool format to bring it close to feature parity with XML tools, and strips inherently unsafe elements, which should eventually allow a subset of trusted users to bring their own tools.
I'll follow up with a more extensive description, but here's a screenshot of the embedded tool editor.
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