Updated to new template

Author: glatard

boutiques/README.md

@@ -1,4 +1,4 @@
-# Boutiques descriptors
+# Boutiques descriptor
 
 This directory contains a
 [Boutiques](https://github.com/boutiques/boutiques) descriptor for the

boutiques/bids-app-example.json

@@ -1,58 +1,67 @@
 {
-    "name" : "Example BIDS app",
-    "tool-version" : "0.0.6",
+    "name" : "example",
+    "tool-version" : "dev",
     "description" : "See https://github.com/BIDS-Apps/example",
-    "command-line" : "mkdir -p [OUTPUT_DIR_NAME]; /run.py [BIDS_DIR] [OUTPUT_DIR_NAME] [ANALYSIS_LEVEL] [PARTICIPANT_LABEL]",
+    "command-line" : "mkdir -p OUTPUT_DIR; /run.py BIDS_DIR OUTPUT_DIR ANALYSIS_LEVEL PARTICIPANT_LABEL SESSION_LABEL",
     "container-image": {
         "type": "docker",
         "image": "bids/example"
     },
-    "schema-version" : "0.4",
+    "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]",
+	"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_NAME]",
+        "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_NAME]",
+	"value-key" : "OUTPUT_DIR",
 	"optional" : true
     },{
 	"id" : "analysis_level",
 	"name" : "Analysis level",
 	"type" : "String",
 	"optional" : false,
-	"value-key" : "[ANALYSIS_LEVEL]",
-	"value-choices" : ["participant", "group"],
+	"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]",
+	"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_NAME]",
+	"path-template" : "OUTPUT_DIR",
         "optional" : false
     }],
     "groups" : [