- 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
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.
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).
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 ;)
| 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 |
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.
| 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 |