Merge pull request #511 from Remi-Gau/API_design

[WIP] API design

Author: Remi-Gau

boutiques/WIP.md

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+# Boutiques descriptor
+
+This directory contains a
+[Boutiques](https://github.com/boutiques/boutiques) descriptor for the
+BIDS app and an example of invocation.
+
+## How to use
+
+* Install Boutiques: `pip install boutiques`
+* Run the example: `bosh ./bids-app-example.json -i ./invocation.json -e -d`
+  (assumes `ds001` is a valid dataset in the current working
+  directory.)

boutiques/cpp_spm.json

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+{
+    "name": "cpp_spm",
+    "command-line": "cpp_spm [InputDataset] [OutputLocation] [AnalysisLevel] [ParticipantLabel] [Action]",
+    "container-image": {
+        "image": "bids/example",
+        "type": "docker"
+    },
+    "description": "See https://github.com/Remi-Gau/bidsNighres.git",
+    "inputs": [
+        {
+            "description": "The directory with the input dataset formatted according to the BIDS standard.",
+            "id": "InputDataset",
+            "name": "Input datasets",
+            "value-key": "[InputDataset]",
+            "type": "File",
+            "list": false,
+            "optional": false,
+            "command-line-flag": "--input-datasets"
+        },
+        {
+            "description": "The directory where the output files should be stored. If you are running a group level analysis, this folder should be prepopulated with the results of the participant level analysis.",
+            "id": "OutputLocation",
+            "name": "Output location",
+            "value-key": "[OutputLocation]",
+            "type": "File",
+            "list": false,
+            "optional": false,
+            "command-line-flag": "--output-location"
+        },
+        {
+            "description": "Level of the analysis that will be performed. Multiple participant level analyses can be run independently (in parallel).",
+            "id": "AnalysisLevel",
+            "name": "Analysis level",
+            "value-key": "[AnalysisLevel]",
+            "type": "String",
+            "optional": false,
+            "list": false,
+            "value-choices": [
+                "subject",
+                "dataset"
+            ],
+            "default": "subject",
+            "command-line-flag": "--analysis-level"
+        },
+        {
+            "description": "The label(s) of the participant(s) that should be analyzed. The label corresponds to sub-<participant_label> from the BIDS spec (so it does not include \"sub-\"). If this parameter is not provided all subjects will be analyzed. Multiple participants can be specified with a space separated list.",
+            "id": "SubjectLabel",
+            "name": "Subject labels",
+            "value-key": "[SubjectLabel]",
+            "type": "String",
+            "list": true,
+            "optional": false,
+            "command-line-flag": "--participant-label"
+        },
+        {
+            "description": "Action to perform",
+            "id": "Action",
+            "name": "Action",
+            "value-key": "[Action]",
+            "type": "String",
+            "list": false,
+            "value-choices": [
+                "genT1map",
+                "skullstrip",
+                "segment"
+            ],
+            "optional": false,
+            "command-line-flag": "--action"
+        },
+        {
+            "description": " Path to a JSON file to filter input file",
+            "id": "BidsFileFilter",
+            "name": "Bids file filter",
+            "value-key": "[BidsFileFilter]",
+            "type": "File",
+            "default": "",
+            "list": false,
+            "optional": true,
+            "command-line-flag": "--action"
+        },
+        {
+            "description": "for debugging",
+            "id": "DryRun",
+            "name": "Dry run",
+            "value-key": "[DryRun]",
+            "type": "File",
+            "default": false,
+            "list": false,
+            "optional": true,
+            "command-line-flag": "--action"
+        }
+    ],
+    "output-files": [
+        {
+            "description": "The directory where the output files should be stored. If you are running a group level analysis, this folder should be prepopulated with the results of the participant level analysis.",
+            "id": "OutputLocation",
+            "name": "Output location",
+            "optional": false,
+            "path-template": "OutputLocation"
+        }
+    ],
+    "schema-version": "0.5",
+    "tool-version": "dev"
+}

boutiques/invocation.json

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+{
+    "bids_dir": "ds001",
+    "output_dir_name": "example-output",
+    "analysis_level": "subject",
+    "participant_label": [
+        "01"
+    ],
+    "action": "segment"
+}