Boutiques descriptor and example

boutiques/README.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 ./SPM.json -i ./invocation.json -e`
+  (assumes `ds001` is a valid dataset in the current working
+  directory.)

boutiques/SPM.json

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+{
+    "name" : "SPM",
+    "tool-version" : "dev",
+    "description" : "See https://github.com/BIDS-Apps/SPM",
+    "command-line" : "mkdir -p OUTPUT_DIR; /opt/spm12/run.sh BIDS_DIR OUTPUT_DIR ANALYSIS_LEVEL PARTICIPANT_LABEL SESSION_LABEL",
+    "container-image": {
+        "type": "docker",
+        "image": "bids/spm"
+    },
+    "schema-version" : "0.5",
+    "inputs" : [{
+        "id" : "bids_dir",
+        "name" : "BIDS directory",
+        "type" : "File",
+        "description" : "The directory with the input dataset formatted according to the BIDS standard.",
+	"value-key" : "BIDS_DIR",
+        "optional" : false
+
+    }, {
+        "id" : "output_dir_name",
+        "name" : "Output directory name",
+        "type" : "String",
+	"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.",
+        "value-key" : "OUTPUT_DIR",
+        "optional" : true
+    },{
+	"id" : "participant_level_analysis_dir",
+	"name" : "Participants dir",
+	"type" : "File",
+	"description": "Directory containing the output of the participants analysis.",
+	"value-key" : "OUTPUT_DIR",
+	"optional" : true
+    },{
+	"id" : "analysis_level",
+	"name" : "Analysis level",
+	"type" : "String",
+	"optional" : false,
+	"value-key" : "ANALYSIS_LEVEL",
+	"value-choices" : [ "participant", "group", "session" ],
+	"description": "Level of the analysis that will be performed. Multiple participant level analyses can be run independently (in parallel)."
+    },  {
+	"id" : "participant_label",
+	"name" : "Participant label",
+	"type" : "String",
+	"value-key": "PARTICIPANT_LABEL",
+	"command-line-flag": "--participant_label",
+	"list" : true,
+	"optional": true,
+	"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" : "session_label",
+	"name" : "Session label",
+	"type" : "String",
+	"value-key": "SESSION_LABEL",
+	"command-line-flag": "--session_label",
+	"list" : true,
+	"optional": true,
+	"description": "The label(s) of the session(s) that should be analyzed. The label corresponds to ses-<session_label>, an extension of the BIDS spec (so it does not include \"ses-\"). If this parameter is not provided all sessions will be analyzed. Multiple sessions can be specified with a space separated list."
+    }],
+    "output-files" : [{
+        "id" : "output_dir",
+        "name" : "Output directory",
+	"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.",
+	"path-template" : "OUTPUT_DIR",
+        "optional" : false
+    }],
+    "groups" : [
+	{
+	    "id": "output_directory",
+	    "name": "Output Directory",
+	    "members" : [ "output_dir_name", "participant_level_analysis_dir" ],
+	    "description" : "For a participants analysis, an output directory name must be specified. For a group analysis, a directory containing the output of participant-level analyses must be selected. ",
+	    "mutually-exclusive":true,
+	    "one-is-required": true
+	}
+    ]
+}

boutiques/invocation.json

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+{
+    "bids_dir" : "ds001",
+    "output_dir_name" : "example-output",
+    "analysis_level": "participant",
+    "participant_label": "01"
+}