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@Remi-Gau
Remi-Gau committed Oct 6, 2023
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12 changes: 6 additions & 6 deletions src/inputs.md
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Expand Up @@ -10,12 +10,12 @@ fields, described fully in

| Field name | Requirement Level | Data type | Description |
|-------------------|-------------------|-----------|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| command-line-flag | OPTIONAL | String | For non-positional arguments, the flag which is associated with the argument on the command-line. |
| id | REQUIRED | String | The argument ID. Alphanumeric values and underscores only. CamelCase is recommended. |
| list | OPTIONAL | Boolean | Indicates whether or not the input field is a list of inputs. One of {true, false}. If omitted, it will be interpreted as false (for example non-list input). |
| name | REQUIRED | String | Plain text name of input for display. Can contain spaces. |
| optional | OPTIONAL | Boolean | Indicates whether or not the input field is required. One of {true, false}. If omitted, will be interpreted as false (for example non-optional input). |
| type | REQUIRED | String | One of {"String", "File", "Flag", "Number"}. |
| command-line-flag | OPTIONAL | String | For non-positional arguments, the flag which is associated with the argument on the command-line. |
| list | OPTIONAL | Boolean | Indicates whether or not the input field is a list of inputs. One of {true, false}. If omitted, it will be interpreted as false (for example non-list input). |
| optional | OPTIONAL | Boolean | Indicates whether or not the input field is required. One of {true, false}. If omitted, will be interpreted as false (for example non-optional input). |
| value-choices | OPTIONAL | List | List of possible values that the parameter may take. |
| value-key | OPTIONAL | String | String to replace in command-line template string. If specified, this MUST NOT be either a superset or subset of the value-key attribute associated with another object in the descriptor; to ensure this, brackets are typically used (for example "[value]"). |

Expand All @@ -25,12 +25,12 @@ In addition to describing inputs themselves, groups of inputs and their relation

| Field name | Requirement Level | Data type | Description |
|--------------------|-------------------|-----------|--------------------------------------------------------------------------------------------------|
| all-or-none | OPTIONAL | Boolean | True if all parameters included in this group need to be included together. . |
| description | RECOMMENDED | String | Description of the input group. |
| id | REQUIRED | String | A short, unique, informative identifier containing only alphanumeric characters and underscores. |
| members | REQUIRED | List | IDs of the input parameters belonging to this group. |
| mutually-exclusive | OPTIONAL | Boolean | True if only one input in the group may be selected at runtime. |
| name | REQUIRED | String | A human-readable name for the input group. |
| description | RECOMMENDED | String | Description of the input group. |
| all-or-none | OPTIONAL | Boolean | True if all parameters included in this group need to be included together. . |
| mutually-exclusive | OPTIONAL | Boolean | True if only one input in the group may be selected at runtime. |
| one-is-required | OPTIONAL | Boolean | True if at least one of the inputs in the group must be selected. |

## Required arguments
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6 changes: 3 additions & 3 deletions src/outputs.md
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Expand Up @@ -11,12 +11,12 @@ It is RECOMMENDED that BIDS Applications produce BIDS-Derivatives-compliant data

| Field name | Requirement Level | Data type | Description |
|-----------------------------------|-------------------|------------------|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| command-line-flag | OPTIONAL | String | Flag associated with the argument on the command-line. Examples: -o, --output |
| id | REQUIRED | String | A short, unique, informative identifier containing only alphanumeric characters and underscores. Typically used to generate variable names. (should conform ^[0-9,_,a-z,A-Z]*$). Example: "data_file" |
| name | REQUIRED | String | A human-readable output name. Example: 'Supplementary input file for X task'. |
| description | RECOMMENDED | String | A plain-text description of the output-files of the BIDS Application. |
| command-line-flag | OPTIONAL | String | Flag associated with the argument on the command-line. Examples: -o, --output |
| file-template | OPTIONAL | Array of strings | An array of strings that may contain value keys and together populate the self-contained structure of a configuration file. |
| id | REQUIRED | String | A short, unique, informative identifier containing only alphanumeric characters and underscores. Typically used to generate variable names. (should conform ^[0-9,_,a-z,A-Z]*$). Example: "data_file" |
| list | OPTIONAL | Boolean | True if output is a list of values. |
| name | REQUIRED | String | A human-readable output name. Example: 'Supplementary input file for X task'. |
| optional | OPTIONAL | Boolean | True if output may not be produced by the tool. |
| path-template | OPTIONAL | String | Describes the output file path relative to the execution directory. May contain input value keys and wildcards. Example: "xx". |
| path-template-stripped-extensions | OPTIONAL | List | List of file extensions that will be stripped from the input values before being substituted in the path template. Example: [". nii",". nii. gz"]. |
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2 changes: 1 addition & 1 deletion src/ui.md
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Expand Up @@ -67,4 +67,4 @@ The `custom` object has the following defined fields for use in the context of B
|-------------------------|-------------------|-----------|-----------------------------------------------------------------------------------------------------------------------------------------|
| BIDSAppSpecVersion | REQUIRED | String | The version of the BIDS application specification with which the application complies. |
| OutputDataSpecification | OPTIONAL | List | If output data conforms to a standard definition (for example NIDM-1. 1. 0), these data standards may be included as a list of strings. |
| <unspecified> | OPTIONAL | Any | Any key referring to arbitrary metadata that may be relevant or of interest to the application and its users. |
| `<unspecified>` | OPTIONAL | Any | Any key referring to arbitrary metadata that may be relevant or of interest to the application and its users. |

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