pydeface-gear/manifest.json at master · flywheel-apps/pydeface-gear · GitHub

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{
  "name": "pydeface-gear",
  "label": "Pydeface Gear",
  "description": "A gear to remove facial structure from MRI images.",
  "author": "Flywheel",
  "maintainer": "Flywheel <support@flywheel.io>",
  "license": "MIT",
  "url": "https://github.com/flywheel-apps/test-gear",
  "source": "https://github.com/flywheel-apps/pydeface-gear",
  "cite": "https://github.com/poldracklab/pydeface",
  "version": "1.0.0",
  "custom": {
    "docker-image": "flywheel/pydeface-gear:1.0.0",
    "gear-builder": {
      "category": "analysis",
      "image": "flywheel/pydeface-gear:1.0.0"
    }
  },
  "inputs": {
    "infile": {
      "base": "file",
      "description": "input nifti",
      "optional": false,
      "type": {
        "enum": [
          "nifti"
        ]
      }
    },
    "template": {
      "base": "file",
      "description": "Optional template image that will be used as the registration target instead of the default.",
      "optional": true,
      "type": {
        "enum": [
          "nifti"
        ]
      }
    },
    "facemask": {
      "base": "file",
      "description": "Optional face mask image that will be used instead of the default.",
      "optional": true,
      "type": {
        "enum": [
          "nifti"
        ]
      }
    }
  },
  "config": {
    "cost": {
      "type": "string",
      "default": "mutualinfo",
      "description": "FSL-FLIRT cost function",
      "enum": [
        "mutualinfo",
        "corratio",
        "normcorr",
        "normmi",
        "leastsq",
        "labeldiff",
        "bbr"
      ]
    },
    "nocleanup": {
      "type": "boolean",
      "description": "Do not cleanup temporary files. True by default.",
      "default": true
    },
    "verbose": {
      "type": "boolean",
      "description": "Show additional status prints. True by default.",
      "default": true
    }
  },
  "command": "/flywheel/v0/run.py",
  "environment":{
	"CONDA_SHLVL": "1",
	"LC_ALL": "C.UTF-8",
	"CONDA_EXE": "/opt/conda/bin/conda",
	"FSLWISH": "/opt/fsl/bin/fslwish",
	"FSLDIR": "/opt/fsl",
	"LANG": "en_US.UTF-8",
	"HOSTNAME": "d8012530f084",
	"FSLMACHINELIST": "",
	"CONDA_PREFIX": "/opt/conda/envs/neuro",
	"CONDA_DIR": "/opt/conda",
	"FSLTCLSH": "/opt/fsl/bin/fsltclsh",
	"FSLREMOTECALL": "",
	"_CE_M": "",
	"PWD": "/flywheel/v0",
	"HOME": "/root",
	"CONDA_PYTHON_EXE": "/opt/conda/bin/python",
	"FSLLOCKDIR": "",
	"_CE_CONDA": "",
	"FLYWHEEL": "/flywheel/v0",
	"CONDA_PROMPT_MODIFIER": "(neuro) ",
	"FSLGECUDAQ": "cuda.q",
	"ND_ENTRYPOINT": "/neurodocker/startup.sh",
	"TERM": "xterm",
	"SHLVL": "1",
	"PATH": "/opt/conda/envs/neuro/bin:/opt/conda/condabin:/opt/conda/bin:/opt/fsl/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin",
	"CONDA_DEFAULT_ENV": "neuro",
	"FSLOUTPUTTYPE": "NIFTI_GZ",
	"FSLMULTIFILEQUIT": "TRUE",
	"_": "/opt/conda/envs/neuro/bin/python"
  }
}