Loni2cwl
This will be a table mapping LONI Pipeline Engine XML tags to Common Workflow Language syntax.
| LONI XML Tag | Arguments/Attributes | Description | Equivalent Command Line Tool CWL Syntax |
|---|---|---|---|
| pipeline | Tag used to declare pipeline | ||
| version | A version number for the pipeline. | cwlVersion | |
| moduleGroup | A collection of modules; can act as a single node in a workflow. | ||
| module | A single executable in a pipeline. | ||
| name | Name of the executable. | ||
| description | A description of the executable. | ||
| location | Path to the executable. | baseCommand | |
| package | Package the executable belongs to. | ||
| version | Version of the package the executable belongs to. | ||
| executableVersion | Version of the executable that the module wraps. | ||
| executableAuthors | Authors of the executable that the XML module definition wraps. | ||
| author | Author name. Nested within ''executableAuthors'' and ''authors'' | ||
| fullName | Full name. | ||
| Author e-mail. | |||
| website | Author website. | ||
| authors | Authors of XML module definition for LONI Pipeline | ||
| citations | A grouping of multiple citation tags. | ||
| citation | Unnamed string containing citation text. | Article citation. Nested within ''citations'' | |
| tag | Tag used to identify the module using LONI Pipeline's search functionality. | ||
| input/output | An input or output parameter | inputs/outputs | |
| name | A name for the input parameter. | ||
| description | A description for the input parameter. | ||
| enabled | Whether or not a particular parameter is enabled for usage as part of the module. | ||
| required | Whether or not the input parameter is required for the module to execute. | ||
| order | The order in which a parameter should appear on the command line (0-indexed). | ||
| switch | The switch used on the command line (e.g., ''-input'') | ||
| switchSpaced | Should there be a space between a switch and its arguments? | ||
| format | Defines the nature of the data accepted/produced by the parameter. | format | |
| type | Type of data produced/accepted by parameter. Choose from the following options: File,Directory,String ,Number,Enumerated. If you choose File, ''filetype'' must be defined within ''format''. | ||
| cardinality | How many arguments should be entered after the switch. -1 is infinite (unavailable for output) -2 is the number of arguments passed to the input (unavailable for input) | ||
| base | A base string to be transformed. | ||
| filetypes | A grouping of file types accepted by the input/output. | ||
| filetype | A file type accepted by the input/output. | ||
| name | The human readable name of the file type. | ||
| extension | The extension of the filetype (no ‘.’ required) | ||
| description | A short description of the file type | ||
| need | A nested element within the ''filetype'' tag that contains the extension of any file needed by this type. You can have multiple ''need'' tags within a ''filetype''. | ||
| transform | Allows you to define an output file name using string operations and a base string. | ||
| order | An index value describing at which point the transform should be executed.(?) | ||
| op | subtract,prepend,append,replace |
See: