boutiques_descriptor.json

{
  "name": "APPIAN",
  "tool-version": "1.0",
  "description": "Automated pipeline for analysis of PET images",
  "command-line": "python2 Launcher.py [SCANLEVEL] [GROUPLEVEL] [SOURCE] [TARGET] [PVCMETHOD] [TKAMETHOD] [SCANNER] [RADIOTRACER] [RECONSTRUCTION] [TASK] [SESSION] [RESULTSLABEL] [PVCLABEL] [TKALABEL] [STARTTIME] [SUBJECTS]",
  "schema-version":"0.5",
  "container-image": {
      "type": "docker",
      "image": "tffunck/appian:latest"
  },
  "inputs":[
      {
      "command-line-flag": "--scan-level",
      "id": "scan_level",
      "name": "Scan Level",
      "type": "Flag",
      "value-key": "[SCANLEVEL]",
      "optional": true  
      },
    {
      "command-line-flag": "--group-level",
      "id": "group_level",
      "name": "Group Level",
      "type": "Flag",
      "value-key": "[GROUPLEVEL]",
      "optional": true  
    },
    {
      "command-line-flag": "--source",
      "id": "source",
      "name": "Source",
      "type": "String",
      "value-key": "[SOURCE]",
      "optional": false
    },
    {
      "command-line-flag": "--target",
      "id": "target",
      "name": "Target",
      "type": "String",
      "value-key": "[TARGET]",
      "optional": false
    },
    {
      "command-line-flag": "--pvc-method",
      "id": "pvc_method",
      "name": "PVC Method",
      "description": "PVC method (default=None)",
      "type": "String",
      "value-key": "[PVCMETHOD]",
      "optional": true,
      "list":false,
      "default-value":"None",
      "value-choices":[
        "None","GTM", "idSURF","LABBE", "RL", "VC", "RBV", "LABBE+RBV", "RBV+VC", "RBV+RL", "LABBE+RBV+VC", "LABBE+RBV+RL", "STC", "MTC", "LABBE+MTC", "MTC+VC", "MTC+RL", "LABBE+MTC+VC", "LABBE+MTC+RL", "IY", "IY+VC", "IY+RL", "MG", "MG+VC", "MG+RL" 
  ]
    },
    {
      "command-line-flag": "--tka-method",
      "id": "tka_type",
      "name": "PVC Type",
      "description": "lp=Logan Plot, pp=Patlak Plot, srtm= Simplified Reference Tissue Model, suv=Simplified Uptake Value, suvr=SUV Ratio (default=None)",
      "type": "String",
      "value-key": "[TKAMETHOD]",
      "optional": true,
      "list":false,
      "default-value":"None",
      "value-choices":[
        "None","lp", "pp", "pp-roi", "srtm", "suv", "suvr"
      ]
    },
    {
      "command-line-flag": "--scanner",
      "id": "scanner",
      "name": "PET Scanner",
      "description": "HR+ , HRRT",
      "type": "String",
      "value-key": "[SCANNER]",
      "optional": false,
      "list":false,
      "value-choices":[
        "HR+", "HRRT"
      ]
    },
    {
      "command-line-flag": "--radiotracer",
      "id": "radiotracer",
      "name": "Radiotracer",
      "description":"String in PET file names that comes after \"_rcl-\" and that identifies the radiotracer of the PET image.",
      "type": "String",
      "value-key": "[RADIOTRACER]",
      "optional": false
    },
    {
      "command-line-flag": "--reconstruction",
      "id": "reconstruction",
      "name": "Reconstruction",
      "description":"String in PET file names that comes after \"_rec-\" and that identifies method used to reconstruct PET image.",
      "type": "String",
      "value-key": "[RECONSTRUCTION]",
      "optional": false
    },
    {
      "command-line-flag": "--session",
      "id": "session",
      "name": "Session",
      "description":"Comma-separated list of Strings in PET file names that comes after \"_ses-\" and that identifies the sessions for which to run APPIAN, e.g. \"initial,follow-up,final\"",
      "type": "String",
      "list":true,
      "value-key": "[SESSION]",
      "optional": false
    },
    {
      "command-line-flag": "--task",
      "id": "task",
      "name": "Task",
      "description":"Comma-separated list of Strings in PET file names that comes after \"_task-\" and that identifies the tasks for which to run APPIAN, e.g. \"rest,task1,task2\"",
      "type": "String",
      "list":true,
      "value-key": "[TASK]",
      "optional": false
    },
    {
      "id": "subjects",
      "name": "Subjects",
      "description":"List of subject names",
      "type": "String",
      "list":true,
      "value-key": "[SUBJECTS]",
      "optional": false
    },
    {
      "command-line-flag": "--results-label",
      "id": "results_label",
      "name": "Label Values for Results",
      "description":"List of comma-separated integer values in the results mask that will be used to extract final results",
      "type": "String",
      "list":false,
      "value-key": "[RESULTSLABEL]",
      "optional": false
    },
    {
      "command-line-flag": "--pvc-label",
      "id": "pvc_label",
      "name": "Label Values for PVC",
      "description":"List of comma-separated integer values in the PVC mask that will be used to extract final PVC values",
      "type": "String",
      "list":false,
      "value-key": "[PVCLABEL]",
      "optional": true
    },
    {
      "command-line-flag": "--tka-label",
      "id": "tka_label",
      "name": "Label Values for TKA",
      "description":"Single integer value in the TKA mask that will be used as a reference region.",
      "type": "String",
      "list":false,
      "value-key": "[TKALABEL]",
      "optional": true
    },
    {
      "command-line-flag": "--start-time",
      "id": "start_time",
      "name": "Start time",
      "description":"Start time for TKA (use if using graphical TKA method).",
      "type":"String",
      "list":false,
      "value-key": "[STARTTIME]",
      "optional": true
    }
  ],
    "output-files": [
    {
    "description": "Output files from APPIAN", 
    "value-key": "[TARGET]", 
    "id": "target_dir", 
    "optional": false, 
    "path-template": "[OUTPUT_BASENAME]", 
    "name": "Output Directory"
    }
    ]
}