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cwltool/schemas/doc/cli-description-languages-comparison.md
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# Comparison of Command Line Interface description languages | ||
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## Compared languages | ||
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* Galaxy v17.05: https://github.com/galaxyproject/galaxy/blob/release_17.05/lib/galaxy/tools/xsd/galaxy.xsd | ||
* CTD v1.7.0 : https://github.com/WorkflowConversion/CTDSchema/blob/Version_1_7_0/CTD.xsd | ||
* CWL v1.0: http://www.commonwl.org/v1.0/CommandLineTool.html / https://github.com/common-workflow-language/common-workflow-language/blob/master/v1.0/CommandLineTool.yml | ||
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## Summary | ||
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### Tool description | ||
CTD reflects the perspective of a tool author targetting the KNIME processing unit approach ("nodes"), whereas | ||
Galaxy reflects the perspective of a platform centered around non-developer users interacting with a graphical interface. | ||
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### Parameters description | ||
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### Data/parameter types | ||
The typing system for parameters in CTD itself is simpler than the other two, providing mainly support for simple types and input/output files, but excluding arrays/lists and complex types. Galaxy adds GUI specific features (`select`, `drill_down`), domain specific features (`color`, `genome_build`, `data_column`), configuration of web services (`base_url`), and tighter integration with workbench internal data management (`library_data`). | ||
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### Command line generation | ||
All of the specifications include a flexible set of possibilities for the generation of command lines, reflecting the effective heterogeneity of the bioinformatics tools ecosystem ;) | ||
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## Comparison table | ||
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### Tool level | ||
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|Galaxy information |Optional |CTD information |Optional |CWL information |Optional | | ||
|---|---|---|---|---|---| | ||
|*description* |X |description |X |label |X | | ||
|*help* |X |*manual* |X |*doc* |X | | ||
|*citation* |X |*citation* (for the underlying tool, DOI or doc URL) |X |*SoftwareRequirement.name.specs* (URI) |X | | ||
| | |*ExecutableName* (overrides the name attribute) |X |*SoftwareRequirement.name.baseCommand[0]* |X | | ||
| | |*ExecutablePath* (specific path to the executable) |X | | | | ||
|*command*+*argument* under parameter | |*CLItype* list of input commands with elements mapping |X | *arguments* and/or *inputBindings* |X | | ||
| | |*logs* (retrospective on execution information - if so probably out of scope)|X | | | | ||
|*tool/outputs/data/@from_work_dir* (name of file to consume) |X |*relocators* (list of parameters, path pairs)|X |*outputBinding* |X | | ||
|*@version* (version of wrapper) |X |*@version* (apprarently version of the tool itself)| |*SoftwareRequirements.name.version* (list of known compatible versions of the underlying tool |X | | ||
|*@name* (just an identifier, not used to build the command itself)||*@name* (also used to build the command itself, unlesss *ExecutableName* is provided)| |baseCommand[0]|X| | ||
|often part of the *help* text|X|*docURL* (URL to documentation)|||| | ||
|*edam_topics* and *edam_operations* - categories are external to tool definition, in per-server config (toolconf.xml)|X|*category* (any string)|X|can use EDAM or other 3rd party annotation or derive via identifier from external registry or datatype| | ||
|(often part of help text)|X|*tags*|X||| | ||
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### Parameter level | ||
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**Important remark** The structure of the CTD file is slightly different, because it explicitely allows the definition of "sub-tools" through a nested structure of NODE/ITEM elements. A node is a subgroup of parameters, and ITEM is a parameter. | ||
Therefore, to focus on Parameter-level information, we consider only the ITEM element here for parameter description in CTD. | ||
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|Galaxy information |Optional |CTD information |Optional |CWL information |Optional | | ||
|---|---|---|---|---|---| | ||
| *param* or *data* | | *ITEM* | | *inputs[n]* or *outputs[n]* | | | ||
|*@name*||*@name*||key of *inp|uts* or *outputs* entry|| | ||
|*@type*||*@type* (Defines the possible types available in the type attribute of ITEM and ITEMLIST.)||type|| | ||
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cwlVersion: v1.0 | ||
class: CommandLineTool | ||
inputs: | ||
- id: "file1" | ||
type: File | ||
default: | ||
class: File | ||
path: default.txt | ||
outputs: [] | ||
arguments: [cat,$(inputs.file1.path)] |
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file1: | ||
class: File | ||
path: hello.txt |
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cwlVersion: v1.0 | ||
class: CommandLineTool | ||
baseCommand: echo | ||
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requirements: | ||
- class: InlineJavascriptRequirement | ||
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inputs: | ||
- id: args.py | ||
type: File | ||
default: | ||
class: File | ||
location: args.py | ||
inputBinding: | ||
position: -1 | ||
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outputs: | ||
- id: args | ||
type: | ||
type: array | ||
items: string | ||
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baseCommand: python | ||
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arguments: | ||
- prefix: -A | ||
valueFrom: $(1+1) | ||
- prefix: -B | ||
valueFrom: $("/foo/bar/baz".split('/').slice(-1)[0]) | ||
- prefix: -C | ||
valueFrom: | | ||
${ | ||
var r = []; | ||
for (var i = 10; i >= 1; i--) { | ||
r.push(i); | ||
} | ||
return r; | ||
} |
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cwlVersion: v1.0 | ||
class: CommandLineTool | ||
inputs: | ||
- id: "file1" | ||
type: File | ||
default: | ||
class: File | ||
path: default.txt | ||
outputs: [] | ||
arguments: [cat,$(inputs.file1.path)] |
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file1: | ||
class: File | ||
path: hello.txt |
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import unittest | ||
from cwltool.load_tool import fetch_document, validate_document | ||
from .util import get_data | ||
from schema_salad.ref_resolver import Loader | ||
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class TestDefaultPath(unittest.TestCase): | ||
# Testing that error is not raised when default path is not present | ||
def test_default_path(self): | ||
document_loader, workflowobj, uri = fetch_document( | ||
get_data("tests/wf/default_path.cwl")) | ||
document_loader, avsc_names, processobj, metadata, uri = validate_document( | ||
document_loader, workflowobj, uri) | ||
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self.assertIsInstance(document_loader,Loader) | ||
self.assertIn("cwlVersion",processobj) |
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cwlVersion: v1.0 | ||
class: CommandLineTool | ||
inputs: | ||
- id: "file1" | ||
type: File | ||
default: | ||
class: File | ||
path: default.txt | ||
outputs: [] | ||
arguments: [cat, $(inputs.file1.path)] | ||
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